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Posted to users@taverna.apache.org by Michele Donato <md...@stanford.edu> on 2017/02/06 19:11:03 UTC
Taverna Workbench crashes on Mac OS
Hello.
I am trying to integrate Taverna workbench in our lab workflows, but I cannot even open it. After installation I try to open it but it crashes immediately
This is the header of the error:
Process: JavaApplicationStub [37612]
Path: /Applications/Taverna Workbench Core 2.5.0.app/Contents/MacOS/JavaApplicationStub
Identifier: net.sf.taverna.t2.workbench
Version: 2.5.0 (2.5.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: JavaApplicationStub [37612]
User ID: 501
Date/Time: 2017-02-06 11:05:06.749 -0800
OS Version: Mac OS X 10.12.2 (16C67)
My colleague tried on a similar system and the software crashes on his system too.
I tried to google the issue but no result was relevant.
Any tip?
Michele
Re: Taverna Workbench crashes on Mac OS
Posted by Ian Dunlop <ia...@gmail.com>.
Hello,
That's great news that you managed to get it started Michele. Maybe it's
not such a good idea for Taverna to bundle Java itself but instead leave
it up to the operating system to provide. We can add your fix somewhere
on the website in case others have this problem.
Cheers,
Ian
On 15/02/17 23:36, Michele Donato wrote:
> Thanks Juande.
>
> I couldn\u2019t make sense of Stian\u2019s message. I already manually installed
> Java on my system, and I did not understand what
>
>>> enable the full JCE encryption or delete your
>>> keychain from ~/Library/Application Support/Taverna*
>
> not
>
>>>
>>> If this works, then you can try to modify the Taverna.app folder and
>>> replace its "jre" folder with a copy of the one you just installed.
>
> meant.
>
> However, simply removing the/Applications/Taverna Workbench Core
> 2.5.0.app/Contents/PlugIns/jre.bundle allowed me to start Taverna Core
> on Mac os 10.12
>
> Michele Donato,
>
> Postdoctoral Fellow,
> Stanford Center for Biomedical Informatics Research (BMIR)
> Department of Medicine
> Stanford University
> 1265 Welch Rd., MSOB X219, Stanford, CA 94305
> Phone: (313) 759 3378
>
>> On Feb 15, 2017, at 02:26, Juande Santander Vela <jdsant@iaa.es
>> <ma...@iaa.es>> wrote:
>>
>> I was able to remove /Applications/Taverna Workbench Core
>> 2.5.0.app/Contents/PlugIns/jre.bundle, and substitute it with a
>> symbolic link to the Java 8 virtual machine in the operating system,
>> on OS X 10.11 El Capitan. Not sure if it will work with macOS Sierra.
>>
>> On Mon, Feb 13, 2017 at 1:51 PM, Stian Soiland-Reyes
>> <stain@apache.org <ma...@apache.org>> wrote:
>>> On Thu, 9 Feb 2017 17:29:14 +0000, Michele Donato
>>> <mdonato@stanford.edu <ma...@stanford.edu>> wrote:
>>>> First of all, thanks for your reply.
>>>>
>>>> One thing to notice, it is not a problem of the retina display, but
>>>> it is related to the graphic card. And, more specifically, Taverna
>>>> does not start with the discrete card, but if I start it with the
>>>> integrated one, and then I switch, everything works correctly. This
>>>> makes me think that whichever component causes the crash it is not
>>>> fundamental to the application.
>>>>
>>>> In any case, I understand that solving this issue leads to a whole
>>>> other sets of issues.
>>>>
>>>> I will follow the development and try to see if the next versions
>>>> work for me.
>>>
>>> I think the Taverna app for Mac OS includes a bundled Java 7
>>> distribution which is probably not updated for the latest Retina
>>> displays.
>>>
>>> Would you be OK testing if it would help help with a newer Java?
>>>
>>> I'm afraid you would have to install it manually.
>>>
>>>
>>> Download from
>>> http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
>>>
>>> You might need to enable the full JCE encryption or delete your
>>> keychain from ~/Library/Application Support/Taverna*
>>>
>>>
>>> Then try the "Standalone" ZIP version of Taverna:
>>> (http://www.taverna.org.uk/download/workbench/2-5/core/#download-binary)
>>>
>>> Start Terminal, try "java -version" first, then
>>> go to the folder where you unpacked the standalone ZIP and
>>> run ./taverna.sh
>>>
>>>
>>> If this works, then you can try to modify the Taverna.app folder and
>>> replace its "jre" folder with a copy of the one you just installed.
>>>
>>>
>>>
>>> --
>>> Stian Soiland-Reyes
>>> University of Manchester
>>> http://www.esciencelab.org.uk/
>>> http://orcid.org/0000-0001-9842-9718
>>>
>>
>>
>>
>> --
>> Juande Santander Vela
>> Instituto de Astrof�sica de Andaluc�a (IAA-CSIC)
>> Glorieta de la Astronom�a s/n, E-18008, Granada, Spain
>
Re: Taverna Workbench crashes on Mac OS
Posted by Michele Donato <md...@stanford.edu>.
Thanks Juande.
I couldn’t make sense of Stian’s message. I already manually installed Java on my system, and I did not understand what
enable the full JCE encryption or delete your
keychain from ~/Library/Application Support/Taverna*
not
If this works, then you can try to modify the Taverna.app folder and
replace its "jre" folder with a copy of the one you just installed.
meant.
However, simply removing the/Applications/Taverna Workbench Core
2.5.0.app/Contents/PlugIns/jre.bundle allowed me to start Taverna Core on Mac os 10.12
Michele Donato,
Postdoctoral Fellow,
Stanford Center for Biomedical Informatics Research (BMIR)
Department of Medicine
Stanford University
1265 Welch Rd., MSOB X219, Stanford, CA 94305
Phone: (313) 759 3378
On Feb 15, 2017, at 02:26, Juande Santander Vela <jd...@iaa.es>> wrote:
I was able to remove /Applications/Taverna Workbench Core
2.5.0.app/Contents/PlugIns/jre.bundle, and substitute it with a
symbolic link to the Java 8 virtual machine in the operating system,
on OS X 10.11 El Capitan. Not sure if it will work with macOS Sierra.
On Mon, Feb 13, 2017 at 1:51 PM, Stian Soiland-Reyes <st...@apache.org>> wrote:
On Thu, 9 Feb 2017 17:29:14 +0000, Michele Donato <md...@stanford.edu>> wrote:
First of all, thanks for your reply.
One thing to notice, it is not a problem of the retina display, but it is related to the graphic card. And, more specifically, Taverna does not start with the discrete card, but if I start it with the integrated one, and then I switch, everything works correctly. This makes me think that whichever component causes the crash it is not fundamental to the application.
In any case, I understand that solving this issue leads to a whole other sets of issues.
I will follow the development and try to see if the next versions work for me.
I think the Taverna app for Mac OS includes a bundled Java 7
distribution which is probably not updated for the latest Retina
displays.
Would you be OK testing if it would help help with a newer Java?
I'm afraid you would have to install it manually.
Download from
http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
You might need to enable the full JCE encryption or delete your
keychain from ~/Library/Application Support/Taverna*
Then try the "Standalone" ZIP version of Taverna:
(http://www.taverna.org.uk/download/workbench/2-5/core/#download-binary)
Start Terminal, try "java -version" first, then
go to the folder where you unpacked the standalone ZIP and
run ./taverna.sh
If this works, then you can try to modify the Taverna.app folder and
replace its "jre" folder with a copy of the one you just installed.
--
Stian Soiland-Reyes
University of Manchester
http://www.esciencelab.org.uk/
http://orcid.org/0000-0001-9842-9718
--
Juande Santander Vela
Instituto de Astrofísica de Andalucía (IAA-CSIC)
Glorieta de la Astronomía s/n, E-18008, Granada, Spain
Re: Taverna Workbench crashes on Mac OS
Posted by Stian Soiland-Reyes <st...@apache.org>.
On Thu, 9 Feb 2017 17:29:14 +0000, Michele Donato <md...@stanford.edu> wrote:
> First of all, thanks for your reply.
>
> One thing to notice, it is not a problem of the retina display, but it is related to the graphic card. And, more specifically, Taverna does not start with the discrete card, but if I start it with the integrated one, and then I switch, everything works correctly. This makes me think that whichever component causes the crash it is not fundamental to the application.
>
> In any case, I understand that solving this issue leads to a whole other sets of issues.
>
> I will follow the development and try to see if the next versions work for me.
I think the Taverna app for Mac OS includes a bundled Java 7
distribution which is probably not updated for the latest Retina
displays.
Would you be OK testing if it would help help with a newer Java?
I'm afraid you would have to install it manually.
Download from
http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
You might need to enable the full JCE encryption or delete your
keychain from ~/Library/Application Support/Taverna*
Then try the "Standalone" ZIP version of Taverna:
(http://www.taverna.org.uk/download/workbench/2-5/core/#download-binary)
Start Terminal, try "java -version" first, then
go to the folder where you unpacked the standalone ZIP and
run ./taverna.sh
If this works, then you can try to modify the Taverna.app folder and
replace its "jre" folder with a copy of the one you just installed.
--
Stian Soiland-Reyes
University of Manchester
http://www.esciencelab.org.uk/
http://orcid.org/0000-0001-9842-9718
Re: Taverna Workbench crashes on Mac OS
Posted by Michele Donato <md...@stanford.edu>.
Hi Donald,
First of all, thanks for your reply.
One thing to notice, it is not a problem of the retina display, but it is related to the graphic card. And, more specifically, Taverna does not start with the discrete card, but if I start it with the integrated one, and then I switch, everything works correctly. This makes me think that whichever component causes the crash it is not fundamental to the application.
In any case, I understand that solving this issue leads to a whole other sets of issues.
I will follow the development and try to see if the next versions work for me.
Best,
Michele
On Feb 9, 2017, at 02:33, Donal K. Fellows <do...@manchester.ac.uk>> wrote:
On 07/02/2017 17:34, Michele Donato wrote:
Any idea how to fix this to have it work without the graphic card
switcharoo trick?
The problem is that it's a weird Java problem, and that's really out of
our league to fix. I've seen font-rendering problems in other simple
Java programs running on Retina displays, so I know it's not linked to
the Taverna code; there's at least a historic problem with the
differences between the handling of the glyph definitions and the
metrics for those glyphs when running on Retina displays, and maybe on
other HighDPI systems too. That there's a crash is bad, but it's hard to
pin it down to anything specific that we're doing wrong; we really don't
do very much over-clever with the GUI, or at least not in a way that
should produce a full process crash (as we just aren't using native code
that way).
The internals of font rendering are *very* complicated, in the “scare me
off every time I look” category (along with regular expression
evaluation engines), so the best that I think is possible at all is to
find an updated JRE and replace the internal version with something that
*might* be fixed. But without changing the major version of the JRE,
since that breaks other things (Taverna's critically dependent on both
security and classloader configuration, and those things *do* change
between major Java versions; one of the goals for Apache Taverna
Workbench is to stop having the worst of these problems, as they're
symptoms of sustainability problems).
I acknowledge that this is a singularly unhelpful message from your
perspective. Sorry about that…
Donal.
<donal_k_fellows.vcf>
Re: Taverna Workbench crashes on Mac OS
Posted by "Donal K. Fellows" <do...@manchester.ac.uk>.
On 07/02/2017 17:34, Michele Donato wrote:
> Any idea how to fix this to have it work without the graphic card
> switcharoo trick?
The problem is that it's a weird Java problem, and that's really out of
our league to fix. I've seen font-rendering problems in other simple
Java programs running on Retina displays, so I know it's not linked to
the Taverna code; there's at least a historic problem with the
differences between the handling of the glyph definitions and the
metrics for those glyphs when running on Retina displays, and maybe on
other HighDPI systems too. That there's a crash is bad, but it's hard to
pin it down to anything specific that we're doing wrong; we really don't
do very much over-clever with the GUI, or at least not in a way that
should produce a full process crash (as we just aren't using native code
that way).
The internals of font rendering are *very* complicated, in the \u201cscare me
off every time I look\u201d category (along with regular expression
evaluation engines), so the best that I think is possible at all is to
find an updated JRE and replace the internal version with something that
*might* be fixed. But without changing the major version of the JRE,
since that breaks other things (Taverna's critically dependent on both
security and classloader configuration, and those things *do* change
between major Java versions; one of the goals for Apache Taverna
Workbench is to stop having the worst of these problems, as they're
symptoms of sustainability problems).
I acknowledge that this is a singularly unhelpful message from your
perspective. Sorry about that\u2026
Donal.
Re: Taverna Workbench crashes on Mac OS
Posted by Michele Donato <md...@stanford.edu>.
Hi Alan,
Thanks for your reply.
I tried the Enterprise version, but unfortunately that version does not work either.
I tried it on a very similar Mac Book Pro (Sierra, 15”, retina, mid 2016) and it does not work on that machine either (both Core and Enterprise).
The curious thing is that one of my colleagues has a MacBook pro 13” (with Sierra, retina, 2014) and it works on that machine.
Looking for the particular exception, I found out some posts that link it to the graphic card, stating that it could happen when the mac works with the discrete card. That would explain why the 13” does not have the problem, as it is always working with the Iris card.
Therefore, I did this: I downloaded the application gfxCardStatus, which allows to manually choose the card to be used, and re-started Taverna, and it started without a problem.
Unfortunately this is a deal breaker for me, as the integrated graphic card is not able to drive efficiently the screen I use in the lab.
One positive aspect is that the app seems to stay open after I switch back to the discrete card. This means that I need to switch to integrated, start Taverna, switch back to discrete, then connect my monitor. Not optimal, but it works.
Any idea how to fix this to have it work without the graphic card switcharoo trick?
Thanks
Michele
On Feb 7, 2017, at 01:54, alaninmcr <al...@googlemail.com>> wrote:
On 06/02/2017 19:11, Michele Donato wrote:
Hello.
Hello
I am trying to integrate Taverna workbench in our lab workflows, but I
cannot even open it. After installation I try to open it but it crashes
immediately
This is the header of the error:
Process: JavaApplicationStub [37612]
Path: /Applications/Taverna Workbench Core
2.5.0.app/Contents/MacOS/JavaApplicationStub
Identifier: net.sf.taverna.t2.workbench
Version: 2.5.0 (2.5.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: JavaApplicationStub [37612]
User ID: 501
Date/Time: 2017-02-06 11:05:06.749 -0800
OS Version: Mac OS X 10.12.2 (16C67)
My colleague tried on a similar system and the software crashes on his
system too.
I tried to google the issue but no result was relevant.
Any tip?
Sorry to hear you are having problems. Can you try with another version of the workbench e.g. the enterprise edition
http://www.taverna.org.uk/download/workbench/2-5/enterprise/#download-mac
That will tell us whether it is a problem that is likely to be specific to the core app.
Michele
Alan
Re: Taverna Workbench crashes on Mac OS
Posted by alaninmcr <al...@googlemail.com>.
On 06/02/2017 19:11, Michele Donato wrote:
> Hello.
Hello
> I am trying to integrate Taverna workbench in our lab workflows, but I
> cannot even open it. After installation I try to open it but it crashes
> immediately
>
> This is the header of the error:
>
>> Process: JavaApplicationStub [37612]
>> Path: /Applications/Taverna Workbench Core
>> 2.5.0.app/Contents/MacOS/JavaApplicationStub
>> Identifier: net.sf.taverna.t2.workbench
>> Version: 2.5.0 (2.5.0)
>> Code Type: X86-64 (Native)
>> Parent Process: ??? [1]
>> Responsible: JavaApplicationStub [37612]
>> User ID: 501
>>
>> Date/Time: 2017-02-06 11:05:06.749 -0800
>> OS Version: Mac OS X 10.12.2 (16C67)
>
> My colleague tried on a similar system and the software crashes on his
> system too.
> I tried to google the issue but no result was relevant.
>
> Any tip?
Sorry to hear you are having problems. Can you try with another version
of the workbench e.g. the enterprise edition
http://www.taverna.org.uk/download/workbench/2-5/enterprise/#download-mac
That will tell us whether it is a problem that is likely to be specific
to the core app.
> Michele
Alan