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Posted to users@jena.apache.org by Cristóbal Miranda <cr...@gmail.com> on 2021/06/21 16:22:25 UTC
tdbloader out of memory error
Hi Jena list.
I've been trying to load wikidata .nt file using tdbloader,
but I'm getting an out of memory error. Last year I was able
to do it with an older version of Jena (not sure if 3.14 or 3.17)
and a bit smaller wikidata file.
Now I'm using jena 4.1 and don't know if this is a bug or
if I did something incorrectly on the way.
I built jena into a docker image and ran
the following command:
>
> docker run -m 120g --cpus=12 -e JVM_ARGS="-Xms8G -Xmx100G" \
> --mount 'type=bind,src=/home/cmiranda/docker-mnts,dst=/external' \
> --name jena-indexing-wikidata cmirandat/jena \
> tdbloader --loc /external/jena-indexed-data
> /external/cache-preprocessing/latest-truthy-3apr2021.nt
Then after some time I had this error on the console:
> 16:39:07 INFO loader :: Elapsed: 63,991.91 seconds [2021/06/20
> 16:39:07 UTC]
> 16:39:10 INFO loader :: Add: 4,227,050,000 triples (Batch:
> 21,561 / Avg: 66,053)
> OpenJDK 64-Bit Server VM warning: INFO:
> os::commit_memory(0x00007f4962e40000, 262144, 0) failed; error='Not enough
> space' (errno=12)
> #
>
> # There is insufficient memory for the Java Runtime Environment to
> continue.
> # Native memory allocation (mmap) failed to map 262144 bytes for
> committing reserved memory.
>
> # An error report file with more information is saved as:
>
> # /jenadir/hs_err_pid8.log
For me it's intriguing that this happens near the 2^32 triples, maybe there
is an overflow somewhere? but this might just be a coincidence.
Some parts of the log file:
>
> # There is insufficient memory for the Java Runtime Environment to
> continue.
> # Native memory allocation (mmap) failed to map 262144 bytes for
> committing reserved memory.
> # Possible reasons:
> # The system is out of physical RAM or swap space
> # Possible solutions:
> # Reduce memory load on the system
> # Increase physical memory or swap space
> # Check if swap backing store is full
> # Decrease Java heap size (-Xmx/-Xms)
> # Decrease number of Java threads
> # Decrease Java thread stack sizes (-Xss)
> # Set larger code cache with -XX:ReservedCodeCacheSize=
> # This output file may be truncated or incomplete.
> #
> # Out of Memory Error (os_linux.cpp:2985), pid=8, tid=9
> #
> # JRE version: OpenJDK Runtime Environment (11.0.11+9) (build
> 11.0.11+9-post-Debian-1deb10u1)
> # Java VM: OpenJDK 64-Bit Server VM (11.0.11+9-post-Debian-1deb10u1, mixed
> mode, tiered, g1 gc, linux-amd64)
> # No core dump will be written. Core dumps have been disabled. To enable
> core dumping, try "ulimit -c unlimited" before starting Java again
> #
> ...
> VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event])
> [0x00007f986c015790] MetaspaceExpand_lock - owner thread:
> 0x00007f986c019800
> OutOfMemory and StackOverflow Exception counts:
> OutOfMemoryError java_heap_errors=2
> LinkageErrors=58
> Heap:
> garbage-first heap total 8388608K, used 198434K [0x00007f7f50000000,
> 0x00007f9850000000)
> region size 16384K, 1 young (16384K), 0 survivors (0K)
> Metaspace used 30487K, capacity 30976K, committed 30976K, reserved
> 32768K
> Heap Regions: E=young(eden), S=young(survivor), O=old,
> HS=humongous(starts), HC=humongous(continues), CS=collection set, F=free,
> A=archive, TAMS=top-at-mark-start (previous, next)
> | 0|0x00007f7f50000000, 0x00007f7f50ffffd8, 0x00007f7f51000000| 99%| O|
> |TAMS 0x00007f7f50000000, 0x00007f7f50000000| Untracked
> | 1|0x00007f7f51000000, 0x00007f7f51b0e3a0, 0x00007f7f52000000| 69%| O|
> |TAMS 0x00007f7f51000000, 0x00007f7f51000000| Untracked
> ...
>
> Internal exceptions (20 events):
> Event: 1.847 Thread 0x00007f986c019800 Implicit null exception at
> 0x00007f985c39c0e8 to 0x00007f985c39c16a
> Event: 1.847 Thread 0x00007f986c019800 Implicit null exception at
> 0x00007f985c35ca2f to 0x00007f985c35ca99
> Event: 1.868 Thread 0x00007f986c019800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f814eef2688}: 'java.lang.Object
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> int)'> (0x00007f814eef2688) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 1.869 Thread 0x00007f986c019800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f814ef03920}: 'java.lang.Object
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> int, int)'> (0x00007f814ef03920) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 1.926 Thread 0x00007f986c019800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f814d260688}: 'java.lang.Object
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, int)'>
> (0x00007f814d260688) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 1.928 Thread 0x00007f986c019800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f814d282b90}: 'java.lang.Object
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, int, int)'>
> (0x00007f814d282b90) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 1.929 Thread 0x00007f986c019800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f814d2a6608}: 'java.lang.Object
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, int, int,
> java.lang.Object)'> (0x00007f814d2a6608) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 1.930 Thread 0x00007f986c019800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f814d2cbca8}: 'java.lang.Object
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, int, int,
> java.lang.Object, java.lang.Object)'> (0x00007f814d2cbca8) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 3.984 Thread 0x00007f986c674800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f814f821eb0}: 'void
> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> java.lang.Object)'> (0x00007f814f821eb0) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 3.986 Thread 0x00007f986c674800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f814f83ab20}: 'java.lang.Object
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> int)'> (0x00007f814f83ab20) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 3.987 Thread 0x00007f986c674800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f814f840168}: 'java.lang.Object
> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> java.lang.Object, int)'> (0x00007f814f840168) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 8.845 Thread 0x00007f986c019800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f81ad9aec20}: 'java.lang.Object
> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
> java.lang.Object, int, int, int, java.lang.Object, java.lang.Object,
> java.lang.Object)'> (0x00007f81ad9aec20) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 8.845 Thread 0x00007f986c019800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f81ad9b32d8}: 'java.lang.Object
> java.lang.invoke.DelegatingMethodHandle$Holder.reinvoke_L(java.lang.Object,
> int, int, int, java.lang.Object, java.lang.Object, java.lang.Object)'>
> (0x00007f81ad9b32d8) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 62.494 Thread 0x00007f986c019800 Implicit null exception at
> 0x00007f985c65c6d1 to 0x00007f985c65cd0c
> Event: 3249.491 Thread 0x00007f986c019800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f829fd2ac48}: 'java.lang.Object
> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
> java.lang.Object, int, int, int, java.lang.Object, int, java.lang.Object,
> java.lang.Object, java.lang.Object)'> (0x00007f829fd2ac48) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 3249.491 Thread 0x00007f986c019800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f829fd2f748}: 'java.lang.Object
> java.lang.invoke.DelegatingMethodHandle$Holder.reinvoke_L(java.lang.Object,
> int, int, int, java.lang.Object, int, java.lang.Object, java.lang.Object,
> java.lang.Object)'> (0x00007f829fd2f748) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 3249.495 Thread 0x00007f986c019800 Exception <a
> 'java/lang/NoSuchMethodError'{0x00007f829fdafd30}: 'java.lang.Object
> java.lang.invoke.Invokers$Holder.linkToTargetMethod(java.lang.Object, int,
> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object)'>
> (0x00007f829fdafd30) thrown at
> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> Event: 63996.243 Thread 0x00007f986c019800 Exception <a
> 'java/lang/OutOfMemoryError'{0x00007f83f336f048}: Map failed>
> (0x00007f83f336f048) thrown at [src/hotspot/share/prims/jni.cpp, line 636]
> Event: 64008.399 Thread 0x00007f986c019800 Exception <a
> 'java/lang/OutOfMemoryError'{0x00007f814f000ad8}: Map failed>
> (0x00007f814f000ad8) thrown at [src/hotspot/share/prims/jni.cpp, line 636]
> Event: 64008.415 Thread 0x00007f986c674800 Implicit null exception at
> 0x00007f985c7bb444 to 0x00007f985c7bbd30
> ...
>
> VM Arguments:
> jvm_args: -Xms8G -Xmx100G
> -Dlog4j.configurationFile=file:/RDFJenaServerBase/jenadir/jena/apache-jena/log4j2.properties
> java_command: tdb.tdbloader --loc /external/jena-indexed-data
> /external/cache-preprocessing/latest-truthy-3apr2021.nt
> java_class_path (initial):
> /RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-bundle-4.1.0-javadoc.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jetty-server-9.4.40.v20210413.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-tdb-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-dboe-base-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-shaded-guava-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-text-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-shacl-4.1.0-sources.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-tdb2-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-shacl-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/libthrift-0.14.1.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/lucene-sandbox-8.8.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-core-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/original-jena-fuseki-geosparql-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/log4j-core-2.14.1.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jetty-util-ajax-9.4.40.v20210413.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-fuseki-access-4.1.0-test-sources.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-mem-4.1.0-test-javadoc.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-fuseki-geosparql-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/simpleclient_common-0.9.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-integration-tests-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-arq-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-tdb-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jetty-util-9.4.40.v20210413.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-remote-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-integration-
> ...
>
>
> --------------- S Y S T E M ---------------
> OS:PRETTY_NAME="Debian GNU/Linux 10 (buster)"
> NAME="Debian GNU/Linux"
> VERSION_ID="10"
> VERSION="10 (buster)"
> VERSION_CODENAME=buster
> ID=debian
> HOME_URL="https://www.debian.org/"
> SUPPORT_URL="https://www.debian.org/support"
> BUG_REPORT_URL="https://bugs.debian.org/"
> uname:Linux 5.10.0-0.bpo.5-amd64 #1 SMP Debian 5.10.24-1~bpo10+1
> (2021-03-29) x86_64
> OS uptime: 51 days 16:39 hours
> libc:glibc 2.28 NPTL 2.28
> rlimit (soft/hard): STACK 8192k/infinity , CORE 0k/infinity , NPROC
> infinity/infinity , NOFILE 1048576/1048576 , AS infinity/infinity , CPU
> infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity ,
> MEMLOCK 64k/64k
> load average:4.41 3.31 3.10
> /proc/meminfo:
> MemTotal: 771614128 kB
> MemFree: 4588316 kB
> MemAvailable: 748598400 kB
> Buffers: 1148388 kB
> Cached: 733238364 kB
> SwapCached: 41300 kB
> Active: 332274448 kB
> Inactive: 415663672 kB
> Active(anon): 11943628 kB
> Inactive(anon): 1593996 kB
> Active(file): 320330820 kB
> Inactive(file): 414069676 kB
> Unevictable: 0 kB
> Mlocked: 0 kB
> SwapTotal: 67108860 kB
> SwapFree: 66484988 kB
> Dirty: 74908016 kB
> Writeback: 56 kB
> AnonPages: 13525108 kB
> Mapped: 256622612 kB
> Shmem: 2040 kB
> KReclaimable: 16044104 kB
> Slab: 17857072 kB
> SReclaimable: 16044104 kB
> SUnreclaim: 1812968 kB
> KernelStack: 8832 kB
> PageTables: 1042544 kB
> NFS_Unstable: 0 kB
> Bounce: 0 kB
> WritebackTmp: 0 kB
> CommitLimit: 452915924 kB
> Committed_AS: 23765740 kB
> VmallocTotal: 34359738367 kB
> VmallocUsed: 34012 kB
> VmallocChunk: 0 kB
> Percpu: 10624 kB
> HardwareCorrupted: 0 kB
> AnonHugePages: 13185024 kB
> ShmemHugePages: 0 kB
> ShmemPmdMapped: 0 kB
> FileHugePages: 0 kB
> FilePmdMapped: 0 kB
> HugePages_Total: 0
> HugePages_Free: 0
> HugePages_Rsvd: 0
> HugePages_Surp: 0
> Hugepagesize: 2048 kB
> Hugetlb: 0 kB
> DirectMap4k: 620540 kB
> DirectMap2M: 102180864 kB
> DirectMap1G: 682622976 kB
> /sys/kernel/mm/transparent_hugepage/enabled:
> [always] madvise never
> /sys/kernel/mm/transparent_hugepage/defrag (defrag/compaction efforts
> parameter):
> always defer defer+madvise [madvise] never
> Process Memory:
> Virtual Size: 646288896K (peak: 646288896K)
> Resident Set Size: 269789276K (peak: 269789616K) (anon: 13301076K, file:
> 256488200K, shmem: 0K)
> Swapped out: 579680K
> C-Heap outstanding allocations: 47803K (may have wrapped)
> /proc/sys/kernel/threads-max (system-wide limit on the number of threads):
> 6028021
> /proc/sys/vm/max_map_count (maximum number of memory map areas a process
> may have):
> 65530
> /proc/sys/kernel/pid_max (system-wide limit on number of process
> identifiers):
> 32768
> container (cgroup) information:
> container_type: cgroupv1
> cpu_cpuset_cpus: 0-31
> cpu_memory_nodes: 0
> active_processor_count: 12
> cpu_quota: 1200000
> cpu_period: 100000
> cpu_shares: -1
> memory_limit_in_bytes: 128849018880
> memory_and_swap_limit_in_bytes: 257698037760
> memory_soft_limit_in_bytes: -1
> memory_usage_in_bytes: 128849002496
> memory_max_usage_in_bytes: 128849018880
> Xen hardware-assisted virtualization detected
> Steal ticks since vm start: 88915
> Steal ticks percentage since vm start: 0.000
> CPU:total 32 (initial active 12) (16 cores per cpu, 2 threads per core)
> family 6 model 85 stepping 4 microcode 0x2006a0a, cmov, cx8, fxsr, mmx,
> sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul,
> erms, rtm, 3dnowpref, lzcnt, ht, tsc, bmi1, bmi2, adx, fma
> CPU Model and flags from /proc/cpuinfo:
> model name : Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat
> pse36 clflush acpi mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm
> constant_tsc rep_good nopl cpuid tsc_known_freq pni pclmulqdq ssse3 fma
> cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave
> avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch cpuid_fault
> invpcid_single pti intel_ppin ssbd ibrs ibpb stibp fsgsbase tsc_adjust bmi1
> hle avx2 smep bmi2 erms invpcid rtm mpx avx512f avx512dq rdseed adx smap
> clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves
> pku ospke md_clear flush_l1d
> Online cpus:
> 0-31
> Offline cpus:
> BIOS frequency limitation:
> <Not Available>
> Frequency switch latency (ns):
> <Not Available>
> Available cpu frequencies:
> <Not Available>
> Current governor:
> <Not Available>
> Core performance/turbo boost:
> <Not Available>
> Memory: 4k page, physical 125829120k(4k free), swap 67108860k(66484988k
> free)
> vm_info: OpenJDK 64-Bit Server VM (11.0.11+9-post-Debian-1deb10u1) for
> linux-amd64 JRE (11.0.11+9-post-Debian-1deb10u1), built on Apr 21 2021
> 15:55:49 by "unknown" with gcc 8.3.0
> END.
Sorry for the big logs, I don't know what is the best way to send those
here.
Any help or suggestions would be appreciated.
Cristobal M.
Re: tdbloader out of memory error
Posted by Andy Seaborne <an...@apache.org>.
Hi Cristóbal,
Thanks for letting us know.
Andy
On 23/06/2021 18:24, Cristóbal Miranda wrote:
> Thank you! This seems to have solved the problem so far.
> I tried with -Xmx10G but that is slower for some reason.
>
> On Mon, 21 Jun 2021 at 15:09, Andy Seaborne <an...@apache.org> wrote:
>
>> Hi Cristóbal,
>>
>> https://jena.apache.org/documentation/tdb2/tdb2_cmds.html
>>
>> This was added in the last few days to the documentation - it applies to
>> TDB1 as well.
>>
>> """
>> Loading very large datasets (like Wikidata) with tdb2.tdbloader may
>> sometimes on linux configurations fail with errors like:
>>
>> Native memory allocation (mmap) failed to map NNNNNN bytes for
>> committing reserved memory.
>>
>> This can be avoided by adding a larger value to the vm.max_map_count
>> option. The command sudo sysctl -w vm.max_map_count=262144 updates the
>> value for your current session, or you can persist the change by editing
>> the value in /etc/sysctl.conf or in /etc/sysctl.d/* override files if
>> available.
>> """
>>
>> Looks like you have
>> /proc/sys/vm/max_map_count = 65530
>> from the stats below so it could be this.
>>
>>
>> errno=12 is an error from the OS and may result from other reasons like
>> not enough phsical RAM for the docker container.
>>
>>
>> --
>>
>> Unrelated - you don't need -Xmx100G -- in fact, 8G should be enough.
>> This leaves more space for the memory mapped files.
>>
>> Andy
>>
>> On 21/06/2021 17:22, Cristóbal Miranda wrote:
>>> Hi Jena list.
>>>
>>> I've been trying to load wikidata .nt file using tdbloader,
>>> but I'm getting an out of memory error. Last year I was able
>>> to do it with an older version of Jena (not sure if 3.14 or 3.17)
>>> and a bit smaller wikidata file.
>>>
>>> Now I'm using jena 4.1 and don't know if this is a bug or
>>> if I did something incorrectly on the way.
>>>
>>> I built jena into a docker image and ran
>>> the following command:
>>>
>>>>
>>>> docker run -m 120g --cpus=12 -e JVM_ARGS="-Xms8G -Xmx100G" \
>>>> --mount 'type=bind,src=/home/cmiranda/docker-mnts,dst=/external' \
>>>> --name jena-indexing-wikidata cmirandat/jena \
>>>> tdbloader --loc /external/jena-indexed-data
>>>> /external/cache-preprocessing/latest-truthy-3apr2021.nt
>>>
>>>
>>> Then after some time I had this error on the console:
>>>
>>>
>>>> 16:39:07 INFO loader :: Elapsed: 63,991.91 seconds
>> [2021/06/20
>>>> 16:39:07 UTC]
>>>> 16:39:10 INFO loader :: Add: 4,227,050,000 triples (Batch:
>>>> 21,561 / Avg: 66,053)
>>>> OpenJDK 64-Bit Server VM warning: INFO:
>>>> os::commit_memory(0x00007f4962e40000, 262144, 0) failed; error='Not
>> enough
>>>> space' (errno=12)
>>>> #
>>>>
>>>> # There is insufficient memory for the Java Runtime Environment to
>>>> continue.
>>>> # Native memory allocation (mmap) failed to map 262144 bytes for
>>>> committing reserved memory.
>>>>
>>>> # An error report file with more information is saved as:
>>>>
>>>> # /jenadir/hs_err_pid8.log
>>>
>>>
>>> For me it's intriguing that this happens near the 2^32 triples, maybe
>> there
>>> is an overflow somewhere? but this might just be a coincidence.
>>>
>>> Some parts of the log file:
>>>
>>>>
>>>> # There is insufficient memory for the Java Runtime Environment to
>>>> continue.
>>>> # Native memory allocation (mmap) failed to map 262144 bytes for
>>>> committing reserved memory.
>>>> # Possible reasons:
>>>> # The system is out of physical RAM or swap space
>>>> # Possible solutions:
>>>> # Reduce memory load on the system
>>>> # Increase physical memory or swap space
>>>> # Check if swap backing store is full
>>>> # Decrease Java heap size (-Xmx/-Xms)
>>>> # Decrease number of Java threads
>>>> # Decrease Java thread stack sizes (-Xss)
>>>> # Set larger code cache with -XX:ReservedCodeCacheSize=
>>>> # This output file may be truncated or incomplete.
>>>> #
>>>> # Out of Memory Error (os_linux.cpp:2985), pid=8, tid=9
>>>> #
>>>> # JRE version: OpenJDK Runtime Environment (11.0.11+9) (build
>>>> 11.0.11+9-post-Debian-1deb10u1)
>>>> # Java VM: OpenJDK 64-Bit Server VM (11.0.11+9-post-Debian-1deb10u1,
>> mixed
>>>> mode, tiered, g1 gc, linux-amd64)
>>>> # No core dump will be written. Core dumps have been disabled. To enable
>>>> core dumping, try "ulimit -c unlimited" before starting Java again
>>>> #
>>>> ...
>>>> VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event])
>>>> [0x00007f986c015790] MetaspaceExpand_lock - owner thread:
>>>> 0x00007f986c019800
>>>> OutOfMemory and StackOverflow Exception counts:
>>>> OutOfMemoryError java_heap_errors=2
>>>> LinkageErrors=58
>>>> Heap:
>>>> garbage-first heap total 8388608K, used 198434K [0x00007f7f50000000,
>>>> 0x00007f9850000000)
>>>> region size 16384K, 1 young (16384K), 0 survivors (0K)
>>>> Metaspace used 30487K, capacity 30976K, committed 30976K,
>> reserved
>>>> 32768K
>>>> Heap Regions: E=young(eden), S=young(survivor), O=old,
>>>> HS=humongous(starts), HC=humongous(continues), CS=collection set,
>> F=free,
>>>> A=archive, TAMS=top-at-mark-start (previous, next)
>>>> | 0|0x00007f7f50000000, 0x00007f7f50ffffd8, 0x00007f7f51000000| 99%|
>> O|
>>>> |TAMS 0x00007f7f50000000, 0x00007f7f50000000| Untracked
>>>> | 1|0x00007f7f51000000, 0x00007f7f51b0e3a0, 0x00007f7f52000000| 69%|
>> O|
>>>> |TAMS 0x00007f7f51000000, 0x00007f7f51000000| Untracked
>>>> ...
>>>>
>>>> Internal exceptions (20 events):
>>>> Event: 1.847 Thread 0x00007f986c019800 Implicit null exception at
>>>> 0x00007f985c39c0e8 to 0x00007f985c39c16a
>>>> Event: 1.847 Thread 0x00007f986c019800 Implicit null exception at
>>>> 0x00007f985c35ca2f to 0x00007f985c35ca99
>>>> Event: 1.868 Thread 0x00007f986c019800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f814eef2688}: 'java.lang.Object
>>>>
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>>>> int)'> (0x00007f814eef2688) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 1.869 Thread 0x00007f986c019800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f814ef03920}: 'java.lang.Object
>>>>
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>>>> int, int)'> (0x00007f814ef03920) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 1.926 Thread 0x00007f986c019800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f814d260688}: 'java.lang.Object
>>>>
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, int)'>
>>>> (0x00007f814d260688) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 1.928 Thread 0x00007f986c019800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f814d282b90}: 'java.lang.Object
>>>>
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, int, int)'>
>>>> (0x00007f814d282b90) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 1.929 Thread 0x00007f986c019800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f814d2a6608}: 'java.lang.Object
>>>>
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, int, int,
>>>> java.lang.Object)'> (0x00007f814d2a6608) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 1.930 Thread 0x00007f986c019800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f814d2cbca8}: 'java.lang.Object
>>>>
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, int, int,
>>>> java.lang.Object, java.lang.Object)'> (0x00007f814d2cbca8) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 3.984 Thread 0x00007f986c674800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f814f821eb0}: 'void
>>>>
>> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>>>> java.lang.Object)'> (0x00007f814f821eb0) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 3.986 Thread 0x00007f986c674800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f814f83ab20}: 'java.lang.Object
>>>>
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>>>> int)'> (0x00007f814f83ab20) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 3.987 Thread 0x00007f986c674800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f814f840168}: 'java.lang.Object
>>>>
>> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
>>>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>>>> java.lang.Object, int)'> (0x00007f814f840168) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 8.845 Thread 0x00007f986c019800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f81ad9aec20}: 'java.lang.Object
>>>>
>> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
>>>> java.lang.Object, int, int, int, java.lang.Object, java.lang.Object,
>>>> java.lang.Object)'> (0x00007f81ad9aec20) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 8.845 Thread 0x00007f986c019800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f81ad9b32d8}: 'java.lang.Object
>>>>
>> java.lang.invoke.DelegatingMethodHandle$Holder.reinvoke_L(java.lang.Object,
>>>> int, int, int, java.lang.Object, java.lang.Object, java.lang.Object)'>
>>>> (0x00007f81ad9b32d8) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 62.494 Thread 0x00007f986c019800 Implicit null exception at
>>>> 0x00007f985c65c6d1 to 0x00007f985c65cd0c
>>>> Event: 3249.491 Thread 0x00007f986c019800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f829fd2ac48}: 'java.lang.Object
>>>>
>> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
>>>> java.lang.Object, int, int, int, java.lang.Object, int,
>> java.lang.Object,
>>>> java.lang.Object, java.lang.Object)'> (0x00007f829fd2ac48) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 3249.491 Thread 0x00007f986c019800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f829fd2f748}: 'java.lang.Object
>>>>
>> java.lang.invoke.DelegatingMethodHandle$Holder.reinvoke_L(java.lang.Object,
>>>> int, int, int, java.lang.Object, int, java.lang.Object,
>> java.lang.Object,
>>>> java.lang.Object)'> (0x00007f829fd2f748) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 3249.495 Thread 0x00007f986c019800 Exception <a
>>>> 'java/lang/NoSuchMethodError'{0x00007f829fdafd30}: 'java.lang.Object
>>>> java.lang.invoke.Invokers$Holder.linkToTargetMethod(java.lang.Object,
>> int,
>>>> java.lang.Object, java.lang.Object, java.lang.Object,
>> java.lang.Object)'>
>>>> (0x00007f829fdafd30) thrown at
>>>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>>>> Event: 63996.243 Thread 0x00007f986c019800 Exception <a
>>>> 'java/lang/OutOfMemoryError'{0x00007f83f336f048}: Map failed>
>>>> (0x00007f83f336f048) thrown at [src/hotspot/share/prims/jni.cpp, line
>> 636]
>>>> Event: 64008.399 Thread 0x00007f986c019800 Exception <a
>>>> 'java/lang/OutOfMemoryError'{0x00007f814f000ad8}: Map failed>
>>>> (0x00007f814f000ad8) thrown at [src/hotspot/share/prims/jni.cpp, line
>> 636]
>>>> Event: 64008.415 Thread 0x00007f986c674800 Implicit null exception at
>>>> 0x00007f985c7bb444 to 0x00007f985c7bbd30
>>>> ...
>>>>
>>>> VM Arguments:
>>>> jvm_args: -Xms8G -Xmx100G
>>>>
>> -Dlog4j.configurationFile=file:/RDFJenaServerBase/jenadir/jena/apache-jena/log4j2.properties
>>>> java_command: tdb.tdbloader --loc /external/jena-indexed-data
>>>> /external/cache-preprocessing/latest-truthy-3apr2021.nt
>>>> java_class_path (initial):
>>>>
>> /RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-bundle-4.1.0-javadoc.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jetty-server-9.4.40.v20210413.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-tdb-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-dboe-base-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-shaded-guava-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-text-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-shacl-4.1.0-sources.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-tdb2-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-shacl-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/libthrift-0.14.1.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/lucene-sandbox-8.8.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-core-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/original-jena-fuseki-geosparql-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/log4j-core-2.14.1.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jetty-util-ajax-9.4.40.v20210413.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-fuseki-access-4.1.0-test-sources.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-mem-4.1.0-test-javadoc.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-fuseki-geosparql-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/simpleclient_common-0.9.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-integration-tests-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-arq-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-tdb-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jetty-util-9.4.40.v20210413.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-remote-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-integration-
>>>> ...
>>>>
>>>>
>>>> --------------- S Y S T E M ---------------
>>>> OS:PRETTY_NAME="Debian GNU/Linux 10 (buster)"
>>>> NAME="Debian GNU/Linux"
>>>> VERSION_ID="10"
>>>> VERSION="10 (buster)"
>>>> VERSION_CODENAME=buster
>>>> ID=debian
>>>> HOME_URL="https://www.debian.org/"
>>>> SUPPORT_URL="https://www.debian.org/support"
>>>> BUG_REPORT_URL="https://bugs.debian.org/"
>>>> uname:Linux 5.10.0-0.bpo.5-amd64 #1 SMP Debian 5.10.24-1~bpo10+1
>>>> (2021-03-29) x86_64
>>>> OS uptime: 51 days 16:39 hours
>>>> libc:glibc 2.28 NPTL 2.28
>>>> rlimit (soft/hard): STACK 8192k/infinity , CORE 0k/infinity , NPROC
>>>> infinity/infinity , NOFILE 1048576/1048576 , AS infinity/infinity , CPU
>>>> infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity ,
>>>> MEMLOCK 64k/64k
>>>> load average:4.41 3.31 3.10
>>>> /proc/meminfo:
>>>> MemTotal: 771614128 kB
>>>> MemFree: 4588316 kB
>>>> MemAvailable: 748598400 kB
>>>> Buffers: 1148388 kB
>>>> Cached: 733238364 kB
>>>> SwapCached: 41300 kB
>>>> Active: 332274448 kB
>>>> Inactive: 415663672 kB
>>>> Active(anon): 11943628 kB
>>>> Inactive(anon): 1593996 kB
>>>> Active(file): 320330820 kB
>>>> Inactive(file): 414069676 kB
>>>> Unevictable: 0 kB
>>>> Mlocked: 0 kB
>>>> SwapTotal: 67108860 kB
>>>> SwapFree: 66484988 kB
>>>> Dirty: 74908016 kB
>>>> Writeback: 56 kB
>>>> AnonPages: 13525108 kB
>>>> Mapped: 256622612 kB
>>>> Shmem: 2040 kB
>>>> KReclaimable: 16044104 kB
>>>> Slab: 17857072 kB
>>>> SReclaimable: 16044104 kB
>>>> SUnreclaim: 1812968 kB
>>>> KernelStack: 8832 kB
>>>> PageTables: 1042544 kB
>>>> NFS_Unstable: 0 kB
>>>> Bounce: 0 kB
>>>> WritebackTmp: 0 kB
>>>> CommitLimit: 452915924 kB
>>>> Committed_AS: 23765740 kB
>>>> VmallocTotal: 34359738367 kB
>>>> VmallocUsed: 34012 kB
>>>> VmallocChunk: 0 kB
>>>> Percpu: 10624 kB
>>>> HardwareCorrupted: 0 kB
>>>> AnonHugePages: 13185024 kB
>>>> ShmemHugePages: 0 kB
>>>> ShmemPmdMapped: 0 kB
>>>> FileHugePages: 0 kB
>>>> FilePmdMapped: 0 kB
>>>> HugePages_Total: 0
>>>> HugePages_Free: 0
>>>> HugePages_Rsvd: 0
>>>> HugePages_Surp: 0
>>>> Hugepagesize: 2048 kB
>>>> Hugetlb: 0 kB
>>>> DirectMap4k: 620540 kB
>>>> DirectMap2M: 102180864 kB
>>>> DirectMap1G: 682622976 kB
>>>> /sys/kernel/mm/transparent_hugepage/enabled:
>>>> [always] madvise never
>>>> /sys/kernel/mm/transparent_hugepage/defrag (defrag/compaction efforts
>>>> parameter):
>>>> always defer defer+madvise [madvise] never
>>>> Process Memory:
>>>> Virtual Size: 646288896K (peak: 646288896K)
>>>> Resident Set Size: 269789276K (peak: 269789616K) (anon: 13301076K, file:
>>>> 256488200K, shmem: 0K)
>>>> Swapped out: 579680K
>>>> C-Heap outstanding allocations: 47803K (may have wrapped)
>>>> /proc/sys/kernel/threads-max (system-wide limit on the number of
>> threads):
>>>> 6028021
>>>> /proc/sys/vm/max_map_count (maximum number of memory map areas a process
>>>> may have):
>>>> 65530
>>>> /proc/sys/kernel/pid_max (system-wide limit on number of process
>>>> identifiers):
>>>> 32768
>>>> container (cgroup) information:
>>>> container_type: cgroupv1
>>>> cpu_cpuset_cpus: 0-31
>>>> cpu_memory_nodes: 0
>>>> active_processor_count: 12
>>>> cpu_quota: 1200000
>>>> cpu_period: 100000
>>>> cpu_shares: -1
>>>> memory_limit_in_bytes: 128849018880
>>>> memory_and_swap_limit_in_bytes: 257698037760
>>>> memory_soft_limit_in_bytes: -1
>>>> memory_usage_in_bytes: 128849002496
>>>> memory_max_usage_in_bytes: 128849018880
>>>> Xen hardware-assisted virtualization detected
>>>> Steal ticks since vm start: 88915
>>>> Steal ticks percentage since vm start: 0.000
>>>> CPU:total 32 (initial active 12) (16 cores per cpu, 2 threads per core)
>>>> family 6 model 85 stepping 4 microcode 0x2006a0a, cmov, cx8, fxsr, mmx,
>>>> sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul,
>>>> erms, rtm, 3dnowpref, lzcnt, ht, tsc, bmi1, bmi2, adx, fma
>>>> CPU Model and flags from /proc/cpuinfo:
>>>> model name : Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
>>>> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
>> pat
>>>> pse36 clflush acpi mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm
>>>> constant_tsc rep_good nopl cpuid tsc_known_freq pni pclmulqdq ssse3 fma
>>>> cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave
>>>> avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch cpuid_fault
>>>> invpcid_single pti intel_ppin ssbd ibrs ibpb stibp fsgsbase tsc_adjust
>> bmi1
>>>> hle avx2 smep bmi2 erms invpcid rtm mpx avx512f avx512dq rdseed adx smap
>>>> clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1
>> xsaves
>>>> pku ospke md_clear flush_l1d
>>>> Online cpus:
>>>> 0-31
>>>> Offline cpus:
>>>> BIOS frequency limitation:
>>>> <Not Available>
>>>> Frequency switch latency (ns):
>>>> <Not Available>
>>>> Available cpu frequencies:
>>>> <Not Available>
>>>> Current governor:
>>>> <Not Available>
>>>> Core performance/turbo boost:
>>>> <Not Available>
>>>> Memory: 4k page, physical 125829120k(4k free), swap 67108860k(66484988k
>>>> free)
>>>> vm_info: OpenJDK 64-Bit Server VM (11.0.11+9-post-Debian-1deb10u1) for
>>>> linux-amd64 JRE (11.0.11+9-post-Debian-1deb10u1), built on Apr 21 2021
>>>> 15:55:49 by "unknown" with gcc 8.3.0
>>>> END.
>>>
>>>
>>> Sorry for the big logs, I don't know what is the best way to send those
>>> here.
>>>
>>>
>>> Any help or suggestions would be appreciated.
>>>
>>> Cristobal M.
>>>
>>
>
Re: tdbloader out of memory error
Posted by Cristóbal Miranda <cr...@gmail.com>.
Thank you! This seems to have solved the problem so far.
I tried with -Xmx10G but that is slower for some reason.
On Mon, 21 Jun 2021 at 15:09, Andy Seaborne <an...@apache.org> wrote:
> Hi Cristóbal,
>
> https://jena.apache.org/documentation/tdb2/tdb2_cmds.html
>
> This was added in the last few days to the documentation - it applies to
> TDB1 as well.
>
> """
> Loading very large datasets (like Wikidata) with tdb2.tdbloader may
> sometimes on linux configurations fail with errors like:
>
> Native memory allocation (mmap) failed to map NNNNNN bytes for
> committing reserved memory.
>
> This can be avoided by adding a larger value to the vm.max_map_count
> option. The command sudo sysctl -w vm.max_map_count=262144 updates the
> value for your current session, or you can persist the change by editing
> the value in /etc/sysctl.conf or in /etc/sysctl.d/* override files if
> available.
> """
>
> Looks like you have
> /proc/sys/vm/max_map_count = 65530
> from the stats below so it could be this.
>
>
> errno=12 is an error from the OS and may result from other reasons like
> not enough phsical RAM for the docker container.
>
>
> --
>
> Unrelated - you don't need -Xmx100G -- in fact, 8G should be enough.
> This leaves more space for the memory mapped files.
>
> Andy
>
> On 21/06/2021 17:22, Cristóbal Miranda wrote:
> > Hi Jena list.
> >
> > I've been trying to load wikidata .nt file using tdbloader,
> > but I'm getting an out of memory error. Last year I was able
> > to do it with an older version of Jena (not sure if 3.14 or 3.17)
> > and a bit smaller wikidata file.
> >
> > Now I'm using jena 4.1 and don't know if this is a bug or
> > if I did something incorrectly on the way.
> >
> > I built jena into a docker image and ran
> > the following command:
> >
> >>
> >> docker run -m 120g --cpus=12 -e JVM_ARGS="-Xms8G -Xmx100G" \
> >> --mount 'type=bind,src=/home/cmiranda/docker-mnts,dst=/external' \
> >> --name jena-indexing-wikidata cmirandat/jena \
> >> tdbloader --loc /external/jena-indexed-data
> >> /external/cache-preprocessing/latest-truthy-3apr2021.nt
> >
> >
> > Then after some time I had this error on the console:
> >
> >
> >> 16:39:07 INFO loader :: Elapsed: 63,991.91 seconds
> [2021/06/20
> >> 16:39:07 UTC]
> >> 16:39:10 INFO loader :: Add: 4,227,050,000 triples (Batch:
> >> 21,561 / Avg: 66,053)
> >> OpenJDK 64-Bit Server VM warning: INFO:
> >> os::commit_memory(0x00007f4962e40000, 262144, 0) failed; error='Not
> enough
> >> space' (errno=12)
> >> #
> >>
> >> # There is insufficient memory for the Java Runtime Environment to
> >> continue.
> >> # Native memory allocation (mmap) failed to map 262144 bytes for
> >> committing reserved memory.
> >>
> >> # An error report file with more information is saved as:
> >>
> >> # /jenadir/hs_err_pid8.log
> >
> >
> > For me it's intriguing that this happens near the 2^32 triples, maybe
> there
> > is an overflow somewhere? but this might just be a coincidence.
> >
> > Some parts of the log file:
> >
> >>
> >> # There is insufficient memory for the Java Runtime Environment to
> >> continue.
> >> # Native memory allocation (mmap) failed to map 262144 bytes for
> >> committing reserved memory.
> >> # Possible reasons:
> >> # The system is out of physical RAM or swap space
> >> # Possible solutions:
> >> # Reduce memory load on the system
> >> # Increase physical memory or swap space
> >> # Check if swap backing store is full
> >> # Decrease Java heap size (-Xmx/-Xms)
> >> # Decrease number of Java threads
> >> # Decrease Java thread stack sizes (-Xss)
> >> # Set larger code cache with -XX:ReservedCodeCacheSize=
> >> # This output file may be truncated or incomplete.
> >> #
> >> # Out of Memory Error (os_linux.cpp:2985), pid=8, tid=9
> >> #
> >> # JRE version: OpenJDK Runtime Environment (11.0.11+9) (build
> >> 11.0.11+9-post-Debian-1deb10u1)
> >> # Java VM: OpenJDK 64-Bit Server VM (11.0.11+9-post-Debian-1deb10u1,
> mixed
> >> mode, tiered, g1 gc, linux-amd64)
> >> # No core dump will be written. Core dumps have been disabled. To enable
> >> core dumping, try "ulimit -c unlimited" before starting Java again
> >> #
> >> ...
> >> VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event])
> >> [0x00007f986c015790] MetaspaceExpand_lock - owner thread:
> >> 0x00007f986c019800
> >> OutOfMemory and StackOverflow Exception counts:
> >> OutOfMemoryError java_heap_errors=2
> >> LinkageErrors=58
> >> Heap:
> >> garbage-first heap total 8388608K, used 198434K [0x00007f7f50000000,
> >> 0x00007f9850000000)
> >> region size 16384K, 1 young (16384K), 0 survivors (0K)
> >> Metaspace used 30487K, capacity 30976K, committed 30976K,
> reserved
> >> 32768K
> >> Heap Regions: E=young(eden), S=young(survivor), O=old,
> >> HS=humongous(starts), HC=humongous(continues), CS=collection set,
> F=free,
> >> A=archive, TAMS=top-at-mark-start (previous, next)
> >> | 0|0x00007f7f50000000, 0x00007f7f50ffffd8, 0x00007f7f51000000| 99%|
> O|
> >> |TAMS 0x00007f7f50000000, 0x00007f7f50000000| Untracked
> >> | 1|0x00007f7f51000000, 0x00007f7f51b0e3a0, 0x00007f7f52000000| 69%|
> O|
> >> |TAMS 0x00007f7f51000000, 0x00007f7f51000000| Untracked
> >> ...
> >>
> >> Internal exceptions (20 events):
> >> Event: 1.847 Thread 0x00007f986c019800 Implicit null exception at
> >> 0x00007f985c39c0e8 to 0x00007f985c39c16a
> >> Event: 1.847 Thread 0x00007f986c019800 Implicit null exception at
> >> 0x00007f985c35ca2f to 0x00007f985c35ca99
> >> Event: 1.868 Thread 0x00007f986c019800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f814eef2688}: 'java.lang.Object
> >>
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> >> int)'> (0x00007f814eef2688) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 1.869 Thread 0x00007f986c019800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f814ef03920}: 'java.lang.Object
> >>
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> >> int, int)'> (0x00007f814ef03920) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 1.926 Thread 0x00007f986c019800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f814d260688}: 'java.lang.Object
> >>
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, int)'>
> >> (0x00007f814d260688) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 1.928 Thread 0x00007f986c019800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f814d282b90}: 'java.lang.Object
> >>
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, int, int)'>
> >> (0x00007f814d282b90) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 1.929 Thread 0x00007f986c019800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f814d2a6608}: 'java.lang.Object
> >>
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, int, int,
> >> java.lang.Object)'> (0x00007f814d2a6608) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 1.930 Thread 0x00007f986c019800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f814d2cbca8}: 'java.lang.Object
> >>
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, int, int,
> >> java.lang.Object, java.lang.Object)'> (0x00007f814d2cbca8) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 3.984 Thread 0x00007f986c674800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f814f821eb0}: 'void
> >>
> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> >> java.lang.Object)'> (0x00007f814f821eb0) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 3.986 Thread 0x00007f986c674800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f814f83ab20}: 'java.lang.Object
> >>
> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> >> int)'> (0x00007f814f83ab20) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 3.987 Thread 0x00007f986c674800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f814f840168}: 'java.lang.Object
> >>
> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
> >> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
> >> java.lang.Object, int)'> (0x00007f814f840168) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 8.845 Thread 0x00007f986c019800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f81ad9aec20}: 'java.lang.Object
> >>
> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
> >> java.lang.Object, int, int, int, java.lang.Object, java.lang.Object,
> >> java.lang.Object)'> (0x00007f81ad9aec20) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 8.845 Thread 0x00007f986c019800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f81ad9b32d8}: 'java.lang.Object
> >>
> java.lang.invoke.DelegatingMethodHandle$Holder.reinvoke_L(java.lang.Object,
> >> int, int, int, java.lang.Object, java.lang.Object, java.lang.Object)'>
> >> (0x00007f81ad9b32d8) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 62.494 Thread 0x00007f986c019800 Implicit null exception at
> >> 0x00007f985c65c6d1 to 0x00007f985c65cd0c
> >> Event: 3249.491 Thread 0x00007f986c019800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f829fd2ac48}: 'java.lang.Object
> >>
> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
> >> java.lang.Object, int, int, int, java.lang.Object, int,
> java.lang.Object,
> >> java.lang.Object, java.lang.Object)'> (0x00007f829fd2ac48) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 3249.491 Thread 0x00007f986c019800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f829fd2f748}: 'java.lang.Object
> >>
> java.lang.invoke.DelegatingMethodHandle$Holder.reinvoke_L(java.lang.Object,
> >> int, int, int, java.lang.Object, int, java.lang.Object,
> java.lang.Object,
> >> java.lang.Object)'> (0x00007f829fd2f748) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 3249.495 Thread 0x00007f986c019800 Exception <a
> >> 'java/lang/NoSuchMethodError'{0x00007f829fdafd30}: 'java.lang.Object
> >> java.lang.invoke.Invokers$Holder.linkToTargetMethod(java.lang.Object,
> int,
> >> java.lang.Object, java.lang.Object, java.lang.Object,
> java.lang.Object)'>
> >> (0x00007f829fdafd30) thrown at
> >> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
> >> Event: 63996.243 Thread 0x00007f986c019800 Exception <a
> >> 'java/lang/OutOfMemoryError'{0x00007f83f336f048}: Map failed>
> >> (0x00007f83f336f048) thrown at [src/hotspot/share/prims/jni.cpp, line
> 636]
> >> Event: 64008.399 Thread 0x00007f986c019800 Exception <a
> >> 'java/lang/OutOfMemoryError'{0x00007f814f000ad8}: Map failed>
> >> (0x00007f814f000ad8) thrown at [src/hotspot/share/prims/jni.cpp, line
> 636]
> >> Event: 64008.415 Thread 0x00007f986c674800 Implicit null exception at
> >> 0x00007f985c7bb444 to 0x00007f985c7bbd30
> >> ...
> >>
> >> VM Arguments:
> >> jvm_args: -Xms8G -Xmx100G
> >>
> -Dlog4j.configurationFile=file:/RDFJenaServerBase/jenadir/jena/apache-jena/log4j2.properties
> >> java_command: tdb.tdbloader --loc /external/jena-indexed-data
> >> /external/cache-preprocessing/latest-truthy-3apr2021.nt
> >> java_class_path (initial):
> >>
> /RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-bundle-4.1.0-javadoc.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jetty-server-9.4.40.v20210413.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-tdb-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-dboe-base-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-shaded-guava-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-text-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-shacl-4.1.0-sources.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-tdb2-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-shacl-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/libthrift-0.14.1.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/lucene-sandbox-8.8.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-core-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/original-jena-fuseki-geosparql-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/log4j-core-2.14.1.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jetty-util-ajax-9.4.40.v20210413.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-fuseki-access-4.1.0-test-sources.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-mem-4.1.0-test-javadoc.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-fuseki-geosparql-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/simpleclient_common-0.9.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-integration-tests-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-arq-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-tdb-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jetty-util-9.4.40.v20210413.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-remote-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-integration-
> >> ...
> >>
> >>
> >> --------------- S Y S T E M ---------------
> >> OS:PRETTY_NAME="Debian GNU/Linux 10 (buster)"
> >> NAME="Debian GNU/Linux"
> >> VERSION_ID="10"
> >> VERSION="10 (buster)"
> >> VERSION_CODENAME=buster
> >> ID=debian
> >> HOME_URL="https://www.debian.org/"
> >> SUPPORT_URL="https://www.debian.org/support"
> >> BUG_REPORT_URL="https://bugs.debian.org/"
> >> uname:Linux 5.10.0-0.bpo.5-amd64 #1 SMP Debian 5.10.24-1~bpo10+1
> >> (2021-03-29) x86_64
> >> OS uptime: 51 days 16:39 hours
> >> libc:glibc 2.28 NPTL 2.28
> >> rlimit (soft/hard): STACK 8192k/infinity , CORE 0k/infinity , NPROC
> >> infinity/infinity , NOFILE 1048576/1048576 , AS infinity/infinity , CPU
> >> infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity ,
> >> MEMLOCK 64k/64k
> >> load average:4.41 3.31 3.10
> >> /proc/meminfo:
> >> MemTotal: 771614128 kB
> >> MemFree: 4588316 kB
> >> MemAvailable: 748598400 kB
> >> Buffers: 1148388 kB
> >> Cached: 733238364 kB
> >> SwapCached: 41300 kB
> >> Active: 332274448 kB
> >> Inactive: 415663672 kB
> >> Active(anon): 11943628 kB
> >> Inactive(anon): 1593996 kB
> >> Active(file): 320330820 kB
> >> Inactive(file): 414069676 kB
> >> Unevictable: 0 kB
> >> Mlocked: 0 kB
> >> SwapTotal: 67108860 kB
> >> SwapFree: 66484988 kB
> >> Dirty: 74908016 kB
> >> Writeback: 56 kB
> >> AnonPages: 13525108 kB
> >> Mapped: 256622612 kB
> >> Shmem: 2040 kB
> >> KReclaimable: 16044104 kB
> >> Slab: 17857072 kB
> >> SReclaimable: 16044104 kB
> >> SUnreclaim: 1812968 kB
> >> KernelStack: 8832 kB
> >> PageTables: 1042544 kB
> >> NFS_Unstable: 0 kB
> >> Bounce: 0 kB
> >> WritebackTmp: 0 kB
> >> CommitLimit: 452915924 kB
> >> Committed_AS: 23765740 kB
> >> VmallocTotal: 34359738367 kB
> >> VmallocUsed: 34012 kB
> >> VmallocChunk: 0 kB
> >> Percpu: 10624 kB
> >> HardwareCorrupted: 0 kB
> >> AnonHugePages: 13185024 kB
> >> ShmemHugePages: 0 kB
> >> ShmemPmdMapped: 0 kB
> >> FileHugePages: 0 kB
> >> FilePmdMapped: 0 kB
> >> HugePages_Total: 0
> >> HugePages_Free: 0
> >> HugePages_Rsvd: 0
> >> HugePages_Surp: 0
> >> Hugepagesize: 2048 kB
> >> Hugetlb: 0 kB
> >> DirectMap4k: 620540 kB
> >> DirectMap2M: 102180864 kB
> >> DirectMap1G: 682622976 kB
> >> /sys/kernel/mm/transparent_hugepage/enabled:
> >> [always] madvise never
> >> /sys/kernel/mm/transparent_hugepage/defrag (defrag/compaction efforts
> >> parameter):
> >> always defer defer+madvise [madvise] never
> >> Process Memory:
> >> Virtual Size: 646288896K (peak: 646288896K)
> >> Resident Set Size: 269789276K (peak: 269789616K) (anon: 13301076K, file:
> >> 256488200K, shmem: 0K)
> >> Swapped out: 579680K
> >> C-Heap outstanding allocations: 47803K (may have wrapped)
> >> /proc/sys/kernel/threads-max (system-wide limit on the number of
> threads):
> >> 6028021
> >> /proc/sys/vm/max_map_count (maximum number of memory map areas a process
> >> may have):
> >> 65530
> >> /proc/sys/kernel/pid_max (system-wide limit on number of process
> >> identifiers):
> >> 32768
> >> container (cgroup) information:
> >> container_type: cgroupv1
> >> cpu_cpuset_cpus: 0-31
> >> cpu_memory_nodes: 0
> >> active_processor_count: 12
> >> cpu_quota: 1200000
> >> cpu_period: 100000
> >> cpu_shares: -1
> >> memory_limit_in_bytes: 128849018880
> >> memory_and_swap_limit_in_bytes: 257698037760
> >> memory_soft_limit_in_bytes: -1
> >> memory_usage_in_bytes: 128849002496
> >> memory_max_usage_in_bytes: 128849018880
> >> Xen hardware-assisted virtualization detected
> >> Steal ticks since vm start: 88915
> >> Steal ticks percentage since vm start: 0.000
> >> CPU:total 32 (initial active 12) (16 cores per cpu, 2 threads per core)
> >> family 6 model 85 stepping 4 microcode 0x2006a0a, cmov, cx8, fxsr, mmx,
> >> sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul,
> >> erms, rtm, 3dnowpref, lzcnt, ht, tsc, bmi1, bmi2, adx, fma
> >> CPU Model and flags from /proc/cpuinfo:
> >> model name : Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
> >> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
> pat
> >> pse36 clflush acpi mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm
> >> constant_tsc rep_good nopl cpuid tsc_known_freq pni pclmulqdq ssse3 fma
> >> cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave
> >> avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch cpuid_fault
> >> invpcid_single pti intel_ppin ssbd ibrs ibpb stibp fsgsbase tsc_adjust
> bmi1
> >> hle avx2 smep bmi2 erms invpcid rtm mpx avx512f avx512dq rdseed adx smap
> >> clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1
> xsaves
> >> pku ospke md_clear flush_l1d
> >> Online cpus:
> >> 0-31
> >> Offline cpus:
> >> BIOS frequency limitation:
> >> <Not Available>
> >> Frequency switch latency (ns):
> >> <Not Available>
> >> Available cpu frequencies:
> >> <Not Available>
> >> Current governor:
> >> <Not Available>
> >> Core performance/turbo boost:
> >> <Not Available>
> >> Memory: 4k page, physical 125829120k(4k free), swap 67108860k(66484988k
> >> free)
> >> vm_info: OpenJDK 64-Bit Server VM (11.0.11+9-post-Debian-1deb10u1) for
> >> linux-amd64 JRE (11.0.11+9-post-Debian-1deb10u1), built on Apr 21 2021
> >> 15:55:49 by "unknown" with gcc 8.3.0
> >> END.
> >
> >
> > Sorry for the big logs, I don't know what is the best way to send those
> > here.
> >
> >
> > Any help or suggestions would be appreciated.
> >
> > Cristobal M.
> >
>
Re: tdbloader out of memory error
Posted by Andy Seaborne <an...@apache.org>.
Hi Cristóbal,
https://jena.apache.org/documentation/tdb2/tdb2_cmds.html
This was added in the last few days to the documentation - it applies to
TDB1 as well.
"""
Loading very large datasets (like Wikidata) with tdb2.tdbloader may
sometimes on linux configurations fail with errors like:
Native memory allocation (mmap) failed to map NNNNNN bytes for
committing reserved memory.
This can be avoided by adding a larger value to the vm.max_map_count
option. The command sudo sysctl -w vm.max_map_count=262144 updates the
value for your current session, or you can persist the change by editing
the value in /etc/sysctl.conf or in /etc/sysctl.d/* override files if
available.
"""
Looks like you have
/proc/sys/vm/max_map_count = 65530
from the stats below so it could be this.
errno=12 is an error from the OS and may result from other reasons like
not enough phsical RAM for the docker container.
--
Unrelated - you don't need -Xmx100G -- in fact, 8G should be enough.
This leaves more space for the memory mapped files.
Andy
On 21/06/2021 17:22, Cristóbal Miranda wrote:
> Hi Jena list.
>
> I've been trying to load wikidata .nt file using tdbloader,
> but I'm getting an out of memory error. Last year I was able
> to do it with an older version of Jena (not sure if 3.14 or 3.17)
> and a bit smaller wikidata file.
>
> Now I'm using jena 4.1 and don't know if this is a bug or
> if I did something incorrectly on the way.
>
> I built jena into a docker image and ran
> the following command:
>
>>
>> docker run -m 120g --cpus=12 -e JVM_ARGS="-Xms8G -Xmx100G" \
>> --mount 'type=bind,src=/home/cmiranda/docker-mnts,dst=/external' \
>> --name jena-indexing-wikidata cmirandat/jena \
>> tdbloader --loc /external/jena-indexed-data
>> /external/cache-preprocessing/latest-truthy-3apr2021.nt
>
>
> Then after some time I had this error on the console:
>
>
>> 16:39:07 INFO loader :: Elapsed: 63,991.91 seconds [2021/06/20
>> 16:39:07 UTC]
>> 16:39:10 INFO loader :: Add: 4,227,050,000 triples (Batch:
>> 21,561 / Avg: 66,053)
>> OpenJDK 64-Bit Server VM warning: INFO:
>> os::commit_memory(0x00007f4962e40000, 262144, 0) failed; error='Not enough
>> space' (errno=12)
>> #
>>
>> # There is insufficient memory for the Java Runtime Environment to
>> continue.
>> # Native memory allocation (mmap) failed to map 262144 bytes for
>> committing reserved memory.
>>
>> # An error report file with more information is saved as:
>>
>> # /jenadir/hs_err_pid8.log
>
>
> For me it's intriguing that this happens near the 2^32 triples, maybe there
> is an overflow somewhere? but this might just be a coincidence.
>
> Some parts of the log file:
>
>>
>> # There is insufficient memory for the Java Runtime Environment to
>> continue.
>> # Native memory allocation (mmap) failed to map 262144 bytes for
>> committing reserved memory.
>> # Possible reasons:
>> # The system is out of physical RAM or swap space
>> # Possible solutions:
>> # Reduce memory load on the system
>> # Increase physical memory or swap space
>> # Check if swap backing store is full
>> # Decrease Java heap size (-Xmx/-Xms)
>> # Decrease number of Java threads
>> # Decrease Java thread stack sizes (-Xss)
>> # Set larger code cache with -XX:ReservedCodeCacheSize=
>> # This output file may be truncated or incomplete.
>> #
>> # Out of Memory Error (os_linux.cpp:2985), pid=8, tid=9
>> #
>> # JRE version: OpenJDK Runtime Environment (11.0.11+9) (build
>> 11.0.11+9-post-Debian-1deb10u1)
>> # Java VM: OpenJDK 64-Bit Server VM (11.0.11+9-post-Debian-1deb10u1, mixed
>> mode, tiered, g1 gc, linux-amd64)
>> # No core dump will be written. Core dumps have been disabled. To enable
>> core dumping, try "ulimit -c unlimited" before starting Java again
>> #
>> ...
>> VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event])
>> [0x00007f986c015790] MetaspaceExpand_lock - owner thread:
>> 0x00007f986c019800
>> OutOfMemory and StackOverflow Exception counts:
>> OutOfMemoryError java_heap_errors=2
>> LinkageErrors=58
>> Heap:
>> garbage-first heap total 8388608K, used 198434K [0x00007f7f50000000,
>> 0x00007f9850000000)
>> region size 16384K, 1 young (16384K), 0 survivors (0K)
>> Metaspace used 30487K, capacity 30976K, committed 30976K, reserved
>> 32768K
>> Heap Regions: E=young(eden), S=young(survivor), O=old,
>> HS=humongous(starts), HC=humongous(continues), CS=collection set, F=free,
>> A=archive, TAMS=top-at-mark-start (previous, next)
>> | 0|0x00007f7f50000000, 0x00007f7f50ffffd8, 0x00007f7f51000000| 99%| O|
>> |TAMS 0x00007f7f50000000, 0x00007f7f50000000| Untracked
>> | 1|0x00007f7f51000000, 0x00007f7f51b0e3a0, 0x00007f7f52000000| 69%| O|
>> |TAMS 0x00007f7f51000000, 0x00007f7f51000000| Untracked
>> ...
>>
>> Internal exceptions (20 events):
>> Event: 1.847 Thread 0x00007f986c019800 Implicit null exception at
>> 0x00007f985c39c0e8 to 0x00007f985c39c16a
>> Event: 1.847 Thread 0x00007f986c019800 Implicit null exception at
>> 0x00007f985c35ca2f to 0x00007f985c35ca99
>> Event: 1.868 Thread 0x00007f986c019800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f814eef2688}: 'java.lang.Object
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>> int)'> (0x00007f814eef2688) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 1.869 Thread 0x00007f986c019800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f814ef03920}: 'java.lang.Object
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>> int, int)'> (0x00007f814ef03920) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 1.926 Thread 0x00007f986c019800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f814d260688}: 'java.lang.Object
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, int)'>
>> (0x00007f814d260688) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 1.928 Thread 0x00007f986c019800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f814d282b90}: 'java.lang.Object
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, int, int)'>
>> (0x00007f814d282b90) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 1.929 Thread 0x00007f986c019800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f814d2a6608}: 'java.lang.Object
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, int, int,
>> java.lang.Object)'> (0x00007f814d2a6608) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 1.930 Thread 0x00007f986c019800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f814d2cbca8}: 'java.lang.Object
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, int, int,
>> java.lang.Object, java.lang.Object)'> (0x00007f814d2cbca8) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 3.984 Thread 0x00007f986c674800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f814f821eb0}: 'void
>> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>> java.lang.Object)'> (0x00007f814f821eb0) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 3.986 Thread 0x00007f986c674800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f814f83ab20}: 'java.lang.Object
>> java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>> int)'> (0x00007f814f83ab20) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 3.987 Thread 0x00007f986c674800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f814f840168}: 'java.lang.Object
>> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object,
>> java.lang.Object, int)'> (0x00007f814f840168) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 8.845 Thread 0x00007f986c019800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f81ad9aec20}: 'java.lang.Object
>> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
>> java.lang.Object, int, int, int, java.lang.Object, java.lang.Object,
>> java.lang.Object)'> (0x00007f81ad9aec20) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 8.845 Thread 0x00007f986c019800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f81ad9b32d8}: 'java.lang.Object
>> java.lang.invoke.DelegatingMethodHandle$Holder.reinvoke_L(java.lang.Object,
>> int, int, int, java.lang.Object, java.lang.Object, java.lang.Object)'>
>> (0x00007f81ad9b32d8) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 62.494 Thread 0x00007f986c019800 Implicit null exception at
>> 0x00007f985c65c6d1 to 0x00007f985c65cd0c
>> Event: 3249.491 Thread 0x00007f986c019800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f829fd2ac48}: 'java.lang.Object
>> java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object,
>> java.lang.Object, int, int, int, java.lang.Object, int, java.lang.Object,
>> java.lang.Object, java.lang.Object)'> (0x00007f829fd2ac48) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 3249.491 Thread 0x00007f986c019800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f829fd2f748}: 'java.lang.Object
>> java.lang.invoke.DelegatingMethodHandle$Holder.reinvoke_L(java.lang.Object,
>> int, int, int, java.lang.Object, int, java.lang.Object, java.lang.Object,
>> java.lang.Object)'> (0x00007f829fd2f748) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 3249.495 Thread 0x00007f986c019800 Exception <a
>> 'java/lang/NoSuchMethodError'{0x00007f829fdafd30}: 'java.lang.Object
>> java.lang.invoke.Invokers$Holder.linkToTargetMethod(java.lang.Object, int,
>> java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object)'>
>> (0x00007f829fdafd30) thrown at
>> [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
>> Event: 63996.243 Thread 0x00007f986c019800 Exception <a
>> 'java/lang/OutOfMemoryError'{0x00007f83f336f048}: Map failed>
>> (0x00007f83f336f048) thrown at [src/hotspot/share/prims/jni.cpp, line 636]
>> Event: 64008.399 Thread 0x00007f986c019800 Exception <a
>> 'java/lang/OutOfMemoryError'{0x00007f814f000ad8}: Map failed>
>> (0x00007f814f000ad8) thrown at [src/hotspot/share/prims/jni.cpp, line 636]
>> Event: 64008.415 Thread 0x00007f986c674800 Implicit null exception at
>> 0x00007f985c7bb444 to 0x00007f985c7bbd30
>> ...
>>
>> VM Arguments:
>> jvm_args: -Xms8G -Xmx100G
>> -Dlog4j.configurationFile=file:/RDFJenaServerBase/jenadir/jena/apache-jena/log4j2.properties
>> java_command: tdb.tdbloader --loc /external/jena-indexed-data
>> /external/cache-preprocessing/latest-truthy-3apr2021.nt
>> java_class_path (initial):
>> /RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-bundle-4.1.0-javadoc.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jetty-server-9.4.40.v20210413.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-tdb-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-dboe-base-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-shaded-guava-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-text-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-shacl-4.1.0-sources.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-tdb2-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-shacl-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/libthrift-0.14.1.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/lucene-sandbox-8.8.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-core-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/original-jena-fuseki-geosparql-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/log4j-core-2.14.1.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jetty-util-ajax-9.4.40.v20210413.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-fuseki-access-4.1.0-test-sources.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-mem-4.1.0-test-javadoc.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-fuseki-geosparql-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/simpleclient_common-0.9.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-integration-tests-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-arq-4.1.0-tests.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-tdb-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jetty-util-9.4.40.v20210413.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-jdbc-driver-remote-4.1.0.jar:/RDFJenaServerBase/jenadir/jena/apache-jena/lib/jena-integration-
>> ...
>>
>>
>> --------------- S Y S T E M ---------------
>> OS:PRETTY_NAME="Debian GNU/Linux 10 (buster)"
>> NAME="Debian GNU/Linux"
>> VERSION_ID="10"
>> VERSION="10 (buster)"
>> VERSION_CODENAME=buster
>> ID=debian
>> HOME_URL="https://www.debian.org/"
>> SUPPORT_URL="https://www.debian.org/support"
>> BUG_REPORT_URL="https://bugs.debian.org/"
>> uname:Linux 5.10.0-0.bpo.5-amd64 #1 SMP Debian 5.10.24-1~bpo10+1
>> (2021-03-29) x86_64
>> OS uptime: 51 days 16:39 hours
>> libc:glibc 2.28 NPTL 2.28
>> rlimit (soft/hard): STACK 8192k/infinity , CORE 0k/infinity , NPROC
>> infinity/infinity , NOFILE 1048576/1048576 , AS infinity/infinity , CPU
>> infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity ,
>> MEMLOCK 64k/64k
>> load average:4.41 3.31 3.10
>> /proc/meminfo:
>> MemTotal: 771614128 kB
>> MemFree: 4588316 kB
>> MemAvailable: 748598400 kB
>> Buffers: 1148388 kB
>> Cached: 733238364 kB
>> SwapCached: 41300 kB
>> Active: 332274448 kB
>> Inactive: 415663672 kB
>> Active(anon): 11943628 kB
>> Inactive(anon): 1593996 kB
>> Active(file): 320330820 kB
>> Inactive(file): 414069676 kB
>> Unevictable: 0 kB
>> Mlocked: 0 kB
>> SwapTotal: 67108860 kB
>> SwapFree: 66484988 kB
>> Dirty: 74908016 kB
>> Writeback: 56 kB
>> AnonPages: 13525108 kB
>> Mapped: 256622612 kB
>> Shmem: 2040 kB
>> KReclaimable: 16044104 kB
>> Slab: 17857072 kB
>> SReclaimable: 16044104 kB
>> SUnreclaim: 1812968 kB
>> KernelStack: 8832 kB
>> PageTables: 1042544 kB
>> NFS_Unstable: 0 kB
>> Bounce: 0 kB
>> WritebackTmp: 0 kB
>> CommitLimit: 452915924 kB
>> Committed_AS: 23765740 kB
>> VmallocTotal: 34359738367 kB
>> VmallocUsed: 34012 kB
>> VmallocChunk: 0 kB
>> Percpu: 10624 kB
>> HardwareCorrupted: 0 kB
>> AnonHugePages: 13185024 kB
>> ShmemHugePages: 0 kB
>> ShmemPmdMapped: 0 kB
>> FileHugePages: 0 kB
>> FilePmdMapped: 0 kB
>> HugePages_Total: 0
>> HugePages_Free: 0
>> HugePages_Rsvd: 0
>> HugePages_Surp: 0
>> Hugepagesize: 2048 kB
>> Hugetlb: 0 kB
>> DirectMap4k: 620540 kB
>> DirectMap2M: 102180864 kB
>> DirectMap1G: 682622976 kB
>> /sys/kernel/mm/transparent_hugepage/enabled:
>> [always] madvise never
>> /sys/kernel/mm/transparent_hugepage/defrag (defrag/compaction efforts
>> parameter):
>> always defer defer+madvise [madvise] never
>> Process Memory:
>> Virtual Size: 646288896K (peak: 646288896K)
>> Resident Set Size: 269789276K (peak: 269789616K) (anon: 13301076K, file:
>> 256488200K, shmem: 0K)
>> Swapped out: 579680K
>> C-Heap outstanding allocations: 47803K (may have wrapped)
>> /proc/sys/kernel/threads-max (system-wide limit on the number of threads):
>> 6028021
>> /proc/sys/vm/max_map_count (maximum number of memory map areas a process
>> may have):
>> 65530
>> /proc/sys/kernel/pid_max (system-wide limit on number of process
>> identifiers):
>> 32768
>> container (cgroup) information:
>> container_type: cgroupv1
>> cpu_cpuset_cpus: 0-31
>> cpu_memory_nodes: 0
>> active_processor_count: 12
>> cpu_quota: 1200000
>> cpu_period: 100000
>> cpu_shares: -1
>> memory_limit_in_bytes: 128849018880
>> memory_and_swap_limit_in_bytes: 257698037760
>> memory_soft_limit_in_bytes: -1
>> memory_usage_in_bytes: 128849002496
>> memory_max_usage_in_bytes: 128849018880
>> Xen hardware-assisted virtualization detected
>> Steal ticks since vm start: 88915
>> Steal ticks percentage since vm start: 0.000
>> CPU:total 32 (initial active 12) (16 cores per cpu, 2 threads per core)
>> family 6 model 85 stepping 4 microcode 0x2006a0a, cmov, cx8, fxsr, mmx,
>> sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul,
>> erms, rtm, 3dnowpref, lzcnt, ht, tsc, bmi1, bmi2, adx, fma
>> CPU Model and flags from /proc/cpuinfo:
>> model name : Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
>> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat
>> pse36 clflush acpi mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm
>> constant_tsc rep_good nopl cpuid tsc_known_freq pni pclmulqdq ssse3 fma
>> cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave
>> avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch cpuid_fault
>> invpcid_single pti intel_ppin ssbd ibrs ibpb stibp fsgsbase tsc_adjust bmi1
>> hle avx2 smep bmi2 erms invpcid rtm mpx avx512f avx512dq rdseed adx smap
>> clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves
>> pku ospke md_clear flush_l1d
>> Online cpus:
>> 0-31
>> Offline cpus:
>> BIOS frequency limitation:
>> <Not Available>
>> Frequency switch latency (ns):
>> <Not Available>
>> Available cpu frequencies:
>> <Not Available>
>> Current governor:
>> <Not Available>
>> Core performance/turbo boost:
>> <Not Available>
>> Memory: 4k page, physical 125829120k(4k free), swap 67108860k(66484988k
>> free)
>> vm_info: OpenJDK 64-Bit Server VM (11.0.11+9-post-Debian-1deb10u1) for
>> linux-amd64 JRE (11.0.11+9-post-Debian-1deb10u1), built on Apr 21 2021
>> 15:55:49 by "unknown" with gcc 8.3.0
>> END.
>
>
> Sorry for the big logs, I don't know what is the best way to send those
> here.
>
>
> Any help or suggestions would be appreciated.
>
> Cristobal M.
>