You are viewing a plain text version of this content. The canonical link for it is here.
Posted to user@spark.apache.org by Gautham Acharya <ga...@alleninstitute.org> on 2019/07/09 23:22:28 UTC
[Beginner] Run compute on large matrices and return the result in
seconds?
This is my first email to this mailing list, so I apologize if I made any errors.
My team's going to be building an application and I'm investigating some options for distributed compute systems. We want to be performing computes on large matrices.
The requirements are as follows:
1. The matrices can be expected to be up to 50,000 columns x 3 million rows. The values are all integers (except for the row/column headers).
2. The application needs to select a specific row, and calculate the correlation coefficient ( https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.corr.html ) against every other row. This means up to 3 million different calculations.
3. A sorted list of the correlation coefficients and their corresponding row keys need to be returned in under 5 seconds.
4. Users will eventually request random row/column subsets to run calculations on, so precomputing our coefficients is not an option. This needs to be done on request.
I've been looking at many compute solutions, but I'd consider Spark first due to the widespread use and community. I currently have my data loaded into Apache Hbase for a different scenario (random access of rows/columns). I've naively tired loading a dataframe from the CSV using a Spark instance hosted on AWS EMR, but getting the results for even a single correlation takes over 20 seconds.
Thank you!
--gautham
RE: [Beginner] Run compute on large matrices and return the result in
seconds?
Posted by Gautham Acharya <ga...@alleninstitute.org>.
Users can also request random rows in those columns. So a user can request a subset of the matrix (N rows and N columns) which would change the value of the correlation coefficient.
From: Jerry Vinokurov [mailto:grapesmoker@gmail.com]
Sent: Wednesday, July 17, 2019 1:27 PM
To: user@spark.apache.org
Subject: Re: [Beginner] Run compute on large matrices and return the result in seconds?
CAUTION: This email originated from outside the Allen Institute. Please do not click links or open attachments unless you've validated the sender and know the content is safe.
________________________________
Maybe I'm not understanding something about this use case, but why is precomputation not an option? Is it because the matrices themselves change? Because if the matrices are constant, then I think precomputation would work for you even if the users request random correlations. You can just store the resulting column with the matrix id, row, and column as the key for retrieval.
My general impression is that while you could do this in Spark, it's probably not the correct framework for carrying out this kind of operation. This feels more like a job for something like OpenMP than for Spark.
On Wed, Jul 17, 2019 at 3:42 PM Gautham Acharya <ga...@alleninstitute.org>> wrote:
As I said in the my initial message, precomputing is not an option.
Retrieving only the top/bottom N most correlated is an option – would that speed up the results?
Our SLAs are soft – slight variations (+- 15 seconds) will not cause issues.
--gautham
From: Patrick McCarthy [mailto:pmccarthy@dstillery.com<ma...@dstillery.com>]
Sent: Wednesday, July 17, 2019 12:39 PM
To: Gautham Acharya <ga...@alleninstitute.org>>
Cc: Bobby Evans <re...@gmail.com>>; Steven Stetzler <st...@gmail.com>>; user@spark.apache.org<ma...@spark.apache.org>
Subject: Re: [Beginner] Run compute on large matrices and return the result in seconds?
CAUTION: This email originated from outside the Allen Institute. Please do not click links or open attachments unless you've validated the sender and know the content is safe.
________________________________
Do you really need the results of all 3MM computations, or only the top- and bottom-most correlation coefficients? Could correlations be computed on a sample and from that estimate a distribution of coefficients? Would it make sense to precompute offline and instead focus on fast key-value retrieval, like ElasticSearch or ScyllaDB?
Spark is a compute framework rather than a serving backend, I don't think it's designed with retrieval SLAs in mind and you may find those SLAs difficult to maintain.
On Wed, Jul 17, 2019 at 3:14 PM Gautham Acharya <ga...@alleninstitute.org>> wrote:
Thanks for the reply, Bobby.
I’ve received notice that we can probably tolerate response times of up to 30 seconds. Would this be more manageable? 5 seconds was an initial ask, but 20-30 seconds is also a reasonable response time for our use case.
With the new SLA, do you think that we can easily perform this computation in spark?
--gautham
From: Bobby Evans [mailto:revans2@gmail.com<ma...@gmail.com>]
Sent: Wednesday, July 17, 2019 7:06 AM
To: Steven Stetzler <st...@gmail.com>>
Cc: Gautham Acharya <ga...@alleninstitute.org>>; user@spark.apache.org<ma...@spark.apache.org>
Subject: Re: [Beginner] Run compute on large matrices and return the result in seconds?
CAUTION: This email originated from outside the Allen Institute. Please do not click links or open attachments unless you've validated the sender and know the content is safe.
________________________________
Let's do a few quick rules of thumb to get an idea of what kind of processing power you will need in general to do what you want.
You need 3,000,000 ints by 50,000 rows. Each int is 4 bytes so that ends up being about 560 GB that you need to fully process in 5 seconds.
If you are reading this from spinning disks (which average about 80 MB/s) you would need at least 1,450 disks to just read the data in 5 seconds (that number can vary a lot depending on the storage format and your compression ratio).
If you are reading the data over a network (let's say 10GigE even though in practice you cannot get that in the cloud easily) you would need about 90 NICs just to read the data in 5 seconds, again depending on the compression ration this may be lower.
If you assume you have a cluster where it all fits in main memory and have cached all of the data in memory (which in practice I have seen on most modern systems at somewhere between 12 and 16 GB/sec) you would need between 7 and 10 machines just to read through the data once in 5 seconds. Spark also stores cached data compressed so you might need less as well.
All the numbers fit with things that spark should be able to handle, but a 5 second SLA is very tight for this amount of data.
Can you make this work with Spark? probably. Does spark have something built in that will make this fast and simple for you? I doubt it you have some very tight requirements and will likely have to write something custom to make it work the way you want.
On Thu, Jul 11, 2019 at 4:12 PM Steven Stetzler <st...@gmail.com>> wrote:
Hi Gautham,
I am a beginner spark user too and I may not have a complete understanding of your question, but I thought I would start a discussion anyway. Have you looked into using Spark's built in Correlation function? (https://spark.apache.org/docs/latest/ml-statistics.html<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fspark.apache.org%2Fdocs%2Flatest%2Fml-statistics.html&data=02%7C01%7C%7C66627034c52c4b439bf008d70af53a3e%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C0%7C636989920678010006&sdata=EXt206eUyVXF1Pw3xSDBCwBL%2FgJlM6IRYKc3e%2Bnz%2BUE%3D&reserved=0>) This might let you get what you want (per-row correlation against the same matrix) without having to deal with parallelizing the computation yourself. Also, I think the question of how quick you can get your results is largely a data access question vs how fast is Spark question. As long as you can exploit data parallelism (i.e. you can partition up your data), Spark will give you a speedup. You can imagine that if you had a large machine with many cores and ~100 GB of RAM (e.g. a m5.12xlarge EC2 instance), you could fit your problem in main memory and perform your computation with thread based parallelism. This might get your result relatively quickly. For a dedicated application with well constrained memory and compute requirements, it might not be a bad option to do everything on one machine as well. Accessing an external database and distributing work over a large number of computers can add overhead that might be out of your control.
Thanks,
Steven
On Thu, Jul 11, 2019 at 9:24 AM Gautham Acharya <ga...@alleninstitute.org>> wrote:
Ping? I would really appreciate advice on this! Thank you!
From: Gautham Acharya
Sent: Tuesday, July 9, 2019 4:22 PM
To: user@spark.apache.org<ma...@spark.apache.org>
Subject: [Beginner] Run compute on large matrices and return the result in seconds?
This is my first email to this mailing list, so I apologize if I made any errors.
My team's going to be building an application and I'm investigating some options for distributed compute systems. We want to be performing computes on large matrices.
The requirements are as follows:
1. The matrices can be expected to be up to 50,000 columns x 3 million rows. The values are all integers (except for the row/column headers).
2. The application needs to select a specific row, and calculate the correlation coefficient ( https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.corr.html<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpandas.pydata.org%2Fpandas-docs%2Fstable%2Freference%2Fapi%2Fpandas.DataFrame.corr.html&data=02%7C01%7C%7C66627034c52c4b439bf008d70af53a3e%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C0%7C636989920678020014&sdata=zrb6RnbLvteKoJXmwsv5oe2R7adrfmXNNDQP3GTrc7o%3D&reserved=0> ) against every other row. This means up to 3 million different calculations.
3. A sorted list of the correlation coefficients and their corresponding row keys need to be returned in under 5 seconds.
4. Users will eventually request random row/column subsets to run calculations on, so precomputing our coefficients is not an option. This needs to be done on request.
I've been looking at many compute solutions, but I'd consider Spark first due to the widespread use and community. I currently have my data loaded into Apache Hbase for a different scenario (random access of rows/columns). I’ve naively tired loading a dataframe from the CSV using a Spark instance hosted on AWS EMR, but getting the results for even a single correlation takes over 20 seconds.
Thank you!
--gautham
--
Patrick McCarthy
Senior Data Scientist, Machine Learning Engineering
Dstillery
470 Park Ave South, 17th Floor, NYC 10016
--
http://www.google.com/profiles/grapesmoker<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.google.com%2Fprofiles%2Fgrapesmoker&data=02%7C01%7C%7C66627034c52c4b439bf008d70af53a3e%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C0%7C636989920678030019&sdata=mgOpCHm8m%2FgBCcNh%2BDmLodvhxXutDOV08EYPV2tSHEU%3D&reserved=0>
Re: [Beginner] Run compute on large matrices and return the result in seconds?
Posted by Jerry Vinokurov <gr...@gmail.com>.
Maybe I'm not understanding something about this use case, but why is
precomputation not an option? Is it because the matrices themselves change?
Because if the matrices are constant, then I think precomputation would
work for you even if the users request random correlations. You can just
store the resulting column with the matrix id, row, and column as the key
for retrieval.
My general impression is that while you could do this in Spark, it's
probably not the correct framework for carrying out this kind of operation.
This feels more like a job for something like OpenMP than for Spark.
On Wed, Jul 17, 2019 at 3:42 PM Gautham Acharya <ga...@alleninstitute.org>
wrote:
> As I said in the my initial message, precomputing is not an option.
>
>
>
> Retrieving only the top/bottom N most correlated is an option – would that
> speed up the results?
>
>
>
> Our SLAs are soft – slight variations (+- 15 seconds) will not cause
> issues.
>
>
>
> --gautham
>
> *From:* Patrick McCarthy [mailto:pmccarthy@dstillery.com]
> *Sent:* Wednesday, July 17, 2019 12:39 PM
> *To:* Gautham Acharya <ga...@alleninstitute.org>
> *Cc:* Bobby Evans <re...@gmail.com>; Steven Stetzler <
> steven.stetzler@gmail.com>; user@spark.apache.org
> *Subject:* Re: [Beginner] Run compute on large matrices and return the
> result in seconds?
>
>
>
> *CAUTION:* This email originated from outside the Allen Institute. Please
> do not click links or open attachments unless you've validated the sender
> and know the content is safe.
> ------------------------------
>
> Do you really need the results of all 3MM computations, or only the top-
> and bottom-most correlation coefficients? Could correlations be computed on
> a sample and from that estimate a distribution of coefficients? Would it
> make sense to precompute offline and instead focus on fast key-value
> retrieval, like ElasticSearch or ScyllaDB?
>
>
>
> Spark is a compute framework rather than a serving backend, I don't think
> it's designed with retrieval SLAs in mind and you may find those SLAs
> difficult to maintain.
>
>
>
> On Wed, Jul 17, 2019 at 3:14 PM Gautham Acharya <
> gauthama@alleninstitute.org> wrote:
>
> Thanks for the reply, Bobby.
>
>
>
> I’ve received notice that we can probably tolerate response times of up to
> 30 seconds. Would this be more manageable? 5 seconds was an initial ask,
> but 20-30 seconds is also a reasonable response time for our use case.
>
>
>
> With the new SLA, do you think that we can easily perform this computation
> in spark?
>
> --gautham
>
>
>
> *From:* Bobby Evans [mailto:revans2@gmail.com]
> *Sent:* Wednesday, July 17, 2019 7:06 AM
> *To:* Steven Stetzler <st...@gmail.com>
> *Cc:* Gautham Acharya <ga...@alleninstitute.org>; user@spark.apache.org
> *Subject:* Re: [Beginner] Run compute on large matrices and return the
> result in seconds?
>
>
>
> *CAUTION:* This email originated from outside the Allen Institute. Please
> do not click links or open attachments unless you've validated the sender
> and know the content is safe.
> ------------------------------
>
> Let's do a few quick rules of thumb to get an idea of what kind of
> processing power you will need in general to do what you want.
>
>
>
> You need 3,000,000 ints by 50,000 rows. Each int is 4 bytes so that ends
> up being about 560 GB that you need to fully process in 5 seconds.
>
>
>
> If you are reading this from spinning disks (which average about 80 MB/s)
> you would need at least 1,450 disks to just read the data in 5 seconds
> (that number can vary a lot depending on the storage format and your
> compression ratio).
>
> If you are reading the data over a network (let's say 10GigE even though
> in practice you cannot get that in the cloud easily) you would need about
> 90 NICs just to read the data in 5 seconds, again depending on the
> compression ration this may be lower.
>
> If you assume you have a cluster where it all fits in main memory and have
> cached all of the data in memory (which in practice I have seen on most
> modern systems at somewhere between 12 and 16 GB/sec) you would need
> between 7 and 10 machines just to read through the data once in 5 seconds.
> Spark also stores cached data compressed so you might need less as well.
>
>
>
> All the numbers fit with things that spark should be able to handle, but a
> 5 second SLA is very tight for this amount of data.
>
>
>
> Can you make this work with Spark? probably. Does spark have something
> built in that will make this fast and simple for you? I doubt it you have
> some very tight requirements and will likely have to write something custom
> to make it work the way you want.
>
>
>
>
>
> On Thu, Jul 11, 2019 at 4:12 PM Steven Stetzler <st...@gmail.com>
> wrote:
>
> Hi Gautham,
>
>
>
> I am a beginner spark user too and I may not have a complete understanding
> of your question, but I thought I would start a discussion anyway. Have you
> looked into using Spark's built in Correlation function? (
> https://spark.apache.org/docs/latest/ml-statistics.html
> <https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fspark.apache.org%2Fdocs%2Flatest%2Fml-statistics.html&data=02%7C01%7C%7Cabf5672f7ecf4fe1d91808d70aee79bf%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C0%7C636989891687806480&sdata=lDOdQ4kolIDqJ94izPnPvBf0cu9dyizcdKnh0q7B4t8%3D&reserved=0>)
> This might let you get what you want (per-row correlation against the same
> matrix) without having to deal with parallelizing the computation yourself.
> Also, I think the question of how quick you can get your results is largely
> a data access question vs how fast is Spark question. As long as you can
> exploit data parallelism (i.e. you can partition up your data), Spark will
> give you a speedup. You can imagine that if you had a large machine with
> many cores and ~100 GB of RAM (e.g. a m5.12xlarge EC2 instance), you could
> fit your problem in main memory and perform your computation with thread
> based parallelism. This might get your result relatively quickly. For a
> dedicated application with well constrained memory and compute
> requirements, it might not be a bad option to do everything on one machine
> as well. Accessing an external database and distributing work over a large
> number of computers can add overhead that might be out of your control.
>
>
>
> Thanks,
>
> Steven
>
>
>
> On Thu, Jul 11, 2019 at 9:24 AM Gautham Acharya <
> gauthama@alleninstitute.org> wrote:
>
> Ping? I would really appreciate advice on this! Thank you!
>
>
>
> *From:* Gautham Acharya
> *Sent:* Tuesday, July 9, 2019 4:22 PM
> *To:* user@spark.apache.org
> *Subject:* [Beginner] Run compute on large matrices and return the result
> in seconds?
>
>
>
> This is my first email to this mailing list, so I apologize if I made any
> errors.
>
>
>
> My team's going to be building an application and I'm investigating some
> options for distributed compute systems. We want to be performing computes
> on large matrices.
>
>
>
> The requirements are as follows:
>
>
>
> 1. The matrices can be expected to be up to 50,000 columns x 3
> million rows. The values are all integers (except for the row/column
> headers).
>
> 2. The application needs to select a specific row, and calculate the
> correlation coefficient (
> https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.corr.html
> <https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpandas.pydata.org%2Fpandas-docs%2Fstable%2Freference%2Fapi%2Fpandas.DataFrame.corr.html&data=02%7C01%7C%7Cabf5672f7ecf4fe1d91808d70aee79bf%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C0%7C636989891687816477&sdata=X8cov3oI%2FSxiUmS6HCCqQRQsVDC5zem0VW4pzlU%2Bv8E%3D&reserved=0> )
> against every other row. This means up to 3 million different calculations.
>
> 3. A sorted list of the correlation coefficients and their
> corresponding row keys need to be returned in under 5 seconds.
>
> 4. Users will eventually request random row/column subsets to run
> calculations on, so precomputing our coefficients is not an option. This
> needs to be done on request.
>
>
>
> I've been looking at many compute solutions, but I'd consider Spark first
> due to the widespread use and community. I currently have my data loaded
> into Apache Hbase for a different scenario (random access of rows/columns).
> I’ve naively tired loading a dataframe from the CSV using a Spark instance
> hosted on AWS EMR, but getting the results for even a single correlation
> takes over 20 seconds.
>
>
>
> Thank you!
>
>
>
>
>
> --gautham
>
>
>
>
>
> --
>
> *Patrick McCarthy *
>
> Senior Data Scientist, Machine Learning Engineering
>
> Dstillery
>
> 470 Park Ave South, 17th Floor, NYC 10016
>
--
http://www.google.com/profiles/grapesmoker
RE: [Beginner] Run compute on large matrices and return the result in
seconds?
Posted by Gautham Acharya <ga...@alleninstitute.org>.
As I said in the my initial message, precomputing is not an option.
Retrieving only the top/bottom N most correlated is an option – would that speed up the results?
Our SLAs are soft – slight variations (+- 15 seconds) will not cause issues.
--gautham
From: Patrick McCarthy [mailto:pmccarthy@dstillery.com]
Sent: Wednesday, July 17, 2019 12:39 PM
To: Gautham Acharya <ga...@alleninstitute.org>
Cc: Bobby Evans <re...@gmail.com>; Steven Stetzler <st...@gmail.com>; user@spark.apache.org
Subject: Re: [Beginner] Run compute on large matrices and return the result in seconds?
CAUTION: This email originated from outside the Allen Institute. Please do not click links or open attachments unless you've validated the sender and know the content is safe.
________________________________
Do you really need the results of all 3MM computations, or only the top- and bottom-most correlation coefficients? Could correlations be computed on a sample and from that estimate a distribution of coefficients? Would it make sense to precompute offline and instead focus on fast key-value retrieval, like ElasticSearch or ScyllaDB?
Spark is a compute framework rather than a serving backend, I don't think it's designed with retrieval SLAs in mind and you may find those SLAs difficult to maintain.
On Wed, Jul 17, 2019 at 3:14 PM Gautham Acharya <ga...@alleninstitute.org>> wrote:
Thanks for the reply, Bobby.
I’ve received notice that we can probably tolerate response times of up to 30 seconds. Would this be more manageable? 5 seconds was an initial ask, but 20-30 seconds is also a reasonable response time for our use case.
With the new SLA, do you think that we can easily perform this computation in spark?
--gautham
From: Bobby Evans [mailto:revans2@gmail.com<ma...@gmail.com>]
Sent: Wednesday, July 17, 2019 7:06 AM
To: Steven Stetzler <st...@gmail.com>>
Cc: Gautham Acharya <ga...@alleninstitute.org>>; user@spark.apache.org<ma...@spark.apache.org>
Subject: Re: [Beginner] Run compute on large matrices and return the result in seconds?
CAUTION: This email originated from outside the Allen Institute. Please do not click links or open attachments unless you've validated the sender and know the content is safe.
________________________________
Let's do a few quick rules of thumb to get an idea of what kind of processing power you will need in general to do what you want.
You need 3,000,000 ints by 50,000 rows. Each int is 4 bytes so that ends up being about 560 GB that you need to fully process in 5 seconds.
If you are reading this from spinning disks (which average about 80 MB/s) you would need at least 1,450 disks to just read the data in 5 seconds (that number can vary a lot depending on the storage format and your compression ratio).
If you are reading the data over a network (let's say 10GigE even though in practice you cannot get that in the cloud easily) you would need about 90 NICs just to read the data in 5 seconds, again depending on the compression ration this may be lower.
If you assume you have a cluster where it all fits in main memory and have cached all of the data in memory (which in practice I have seen on most modern systems at somewhere between 12 and 16 GB/sec) you would need between 7 and 10 machines just to read through the data once in 5 seconds. Spark also stores cached data compressed so you might need less as well.
All the numbers fit with things that spark should be able to handle, but a 5 second SLA is very tight for this amount of data.
Can you make this work with Spark? probably. Does spark have something built in that will make this fast and simple for you? I doubt it you have some very tight requirements and will likely have to write something custom to make it work the way you want.
On Thu, Jul 11, 2019 at 4:12 PM Steven Stetzler <st...@gmail.com>> wrote:
Hi Gautham,
I am a beginner spark user too and I may not have a complete understanding of your question, but I thought I would start a discussion anyway. Have you looked into using Spark's built in Correlation function? (https://spark.apache.org/docs/latest/ml-statistics.html<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fspark.apache.org%2Fdocs%2Flatest%2Fml-statistics.html&data=02%7C01%7C%7Cabf5672f7ecf4fe1d91808d70aee79bf%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C0%7C636989891687806480&sdata=lDOdQ4kolIDqJ94izPnPvBf0cu9dyizcdKnh0q7B4t8%3D&reserved=0>) This might let you get what you want (per-row correlation against the same matrix) without having to deal with parallelizing the computation yourself. Also, I think the question of how quick you can get your results is largely a data access question vs how fast is Spark question. As long as you can exploit data parallelism (i.e. you can partition up your data), Spark will give you a speedup. You can imagine that if you had a large machine with many cores and ~100 GB of RAM (e.g. a m5.12xlarge EC2 instance), you could fit your problem in main memory and perform your computation with thread based parallelism. This might get your result relatively quickly. For a dedicated application with well constrained memory and compute requirements, it might not be a bad option to do everything on one machine as well. Accessing an external database and distributing work over a large number of computers can add overhead that might be out of your control.
Thanks,
Steven
On Thu, Jul 11, 2019 at 9:24 AM Gautham Acharya <ga...@alleninstitute.org>> wrote:
Ping? I would really appreciate advice on this! Thank you!
From: Gautham Acharya
Sent: Tuesday, July 9, 2019 4:22 PM
To: user@spark.apache.org<ma...@spark.apache.org>
Subject: [Beginner] Run compute on large matrices and return the result in seconds?
This is my first email to this mailing list, so I apologize if I made any errors.
My team's going to be building an application and I'm investigating some options for distributed compute systems. We want to be performing computes on large matrices.
The requirements are as follows:
1. The matrices can be expected to be up to 50,000 columns x 3 million rows. The values are all integers (except for the row/column headers).
2. The application needs to select a specific row, and calculate the correlation coefficient ( https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.corr.html<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpandas.pydata.org%2Fpandas-docs%2Fstable%2Freference%2Fapi%2Fpandas.DataFrame.corr.html&data=02%7C01%7C%7Cabf5672f7ecf4fe1d91808d70aee79bf%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C0%7C636989891687816477&sdata=X8cov3oI%2FSxiUmS6HCCqQRQsVDC5zem0VW4pzlU%2Bv8E%3D&reserved=0> ) against every other row. This means up to 3 million different calculations.
3. A sorted list of the correlation coefficients and their corresponding row keys need to be returned in under 5 seconds.
4. Users will eventually request random row/column subsets to run calculations on, so precomputing our coefficients is not an option. This needs to be done on request.
I've been looking at many compute solutions, but I'd consider Spark first due to the widespread use and community. I currently have my data loaded into Apache Hbase for a different scenario (random access of rows/columns). I’ve naively tired loading a dataframe from the CSV using a Spark instance hosted on AWS EMR, but getting the results for even a single correlation takes over 20 seconds.
Thank you!
--gautham
--
Patrick McCarthy
Senior Data Scientist, Machine Learning Engineering
Dstillery
470 Park Ave South, 17th Floor, NYC 10016
Re: [Beginner] Run compute on large matrices and return the result in seconds?
Posted by Patrick McCarthy <pm...@dstillery.com.INVALID>.
Do you really need the results of all 3MM computations, or only the top-
and bottom-most correlation coefficients? Could correlations be computed on
a sample and from that estimate a distribution of coefficients? Would it
make sense to precompute offline and instead focus on fast key-value
retrieval, like ElasticSearch or ScyllaDB?
Spark is a compute framework rather than a serving backend, I don't think
it's designed with retrieval SLAs in mind and you may find those SLAs
difficult to maintain.
On Wed, Jul 17, 2019 at 3:14 PM Gautham Acharya <ga...@alleninstitute.org>
wrote:
> Thanks for the reply, Bobby.
>
>
>
> I’ve received notice that we can probably tolerate response times of up to
> 30 seconds. Would this be more manageable? 5 seconds was an initial ask,
> but 20-30 seconds is also a reasonable response time for our use case.
>
>
>
> With the new SLA, do you think that we can easily perform this computation
> in spark?
>
> --gautham
>
>
>
> *From:* Bobby Evans [mailto:revans2@gmail.com]
> *Sent:* Wednesday, July 17, 2019 7:06 AM
> *To:* Steven Stetzler <st...@gmail.com>
> *Cc:* Gautham Acharya <ga...@alleninstitute.org>; user@spark.apache.org
> *Subject:* Re: [Beginner] Run compute on large matrices and return the
> result in seconds?
>
>
>
> *CAUTION:* This email originated from outside the Allen Institute. Please
> do not click links or open attachments unless you've validated the sender
> and know the content is safe.
> ------------------------------
>
> Let's do a few quick rules of thumb to get an idea of what kind of
> processing power you will need in general to do what you want.
>
>
>
> You need 3,000,000 ints by 50,000 rows. Each int is 4 bytes so that ends
> up being about 560 GB that you need to fully process in 5 seconds.
>
>
>
> If you are reading this from spinning disks (which average about 80 MB/s)
> you would need at least 1,450 disks to just read the data in 5 seconds
> (that number can vary a lot depending on the storage format and your
> compression ratio).
>
> If you are reading the data over a network (let's say 10GigE even though
> in practice you cannot get that in the cloud easily) you would need about
> 90 NICs just to read the data in 5 seconds, again depending on the
> compression ration this may be lower.
>
> If you assume you have a cluster where it all fits in main memory and have
> cached all of the data in memory (which in practice I have seen on most
> modern systems at somewhere between 12 and 16 GB/sec) you would need
> between 7 and 10 machines just to read through the data once in 5 seconds.
> Spark also stores cached data compressed so you might need less as well.
>
>
>
> All the numbers fit with things that spark should be able to handle, but a
> 5 second SLA is very tight for this amount of data.
>
>
>
> Can you make this work with Spark? probably. Does spark have something
> built in that will make this fast and simple for you? I doubt it you have
> some very tight requirements and will likely have to write something custom
> to make it work the way you want.
>
>
>
>
>
> On Thu, Jul 11, 2019 at 4:12 PM Steven Stetzler <st...@gmail.com>
> wrote:
>
> Hi Gautham,
>
>
>
> I am a beginner spark user too and I may not have a complete understanding
> of your question, but I thought I would start a discussion anyway. Have you
> looked into using Spark's built in Correlation function? (
> https://spark.apache.org/docs/latest/ml-statistics.html
> <https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fspark.apache.org%2Fdocs%2Flatest%2Fml-statistics.html&data=02%7C01%7C%7C7d44353d2dd5420bc35108d70abff11d%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C1%7C636989691818858010&sdata=UG7owx%2FyHayKECNbDbfoNV53nJCSlF06Oak1plpi4RY%3D&reserved=0>)
> This might let you get what you want (per-row correlation against the same
> matrix) without having to deal with parallelizing the computation yourself.
> Also, I think the question of how quick you can get your results is largely
> a data access question vs how fast is Spark question. As long as you can
> exploit data parallelism (i.e. you can partition up your data), Spark will
> give you a speedup. You can imagine that if you had a large machine with
> many cores and ~100 GB of RAM (e.g. a m5.12xlarge EC2 instance), you could
> fit your problem in main memory and perform your computation with thread
> based parallelism. This might get your result relatively quickly. For a
> dedicated application with well constrained memory and compute
> requirements, it might not be a bad option to do everything on one machine
> as well. Accessing an external database and distributing work over a large
> number of computers can add overhead that might be out of your control.
>
>
>
> Thanks,
>
> Steven
>
>
>
> On Thu, Jul 11, 2019 at 9:24 AM Gautham Acharya <
> gauthama@alleninstitute.org> wrote:
>
> Ping? I would really appreciate advice on this! Thank you!
>
>
>
> *From:* Gautham Acharya
> *Sent:* Tuesday, July 9, 2019 4:22 PM
> *To:* user@spark.apache.org
> *Subject:* [Beginner] Run compute on large matrices and return the result
> in seconds?
>
>
>
> This is my first email to this mailing list, so I apologize if I made any
> errors.
>
>
>
> My team's going to be building an application and I'm investigating some
> options for distributed compute systems. We want to be performing computes
> on large matrices.
>
>
>
> The requirements are as follows:
>
>
>
> 1. The matrices can be expected to be up to 50,000 columns x 3
> million rows. The values are all integers (except for the row/column
> headers).
>
> 2. The application needs to select a specific row, and calculate the
> correlation coefficient (
> https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.corr.html
> <https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpandas.pydata.org%2Fpandas-docs%2Fstable%2Freference%2Fapi%2Fpandas.DataFrame.corr.html&data=02%7C01%7C%7C7d44353d2dd5420bc35108d70abff11d%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C1%7C636989691818868018&sdata=e5blX8ItE1JDJRx9D3FnmsXp4TnOKvyH6fA6%2Fw2QTbI%3D&reserved=0> )
> against every other row. This means up to 3 million different calculations.
>
> 3. A sorted list of the correlation coefficients and their
> corresponding row keys need to be returned in under 5 seconds.
>
> 4. Users will eventually request random row/column subsets to run
> calculations on, so precomputing our coefficients is not an option. This
> needs to be done on request.
>
>
>
> I've been looking at many compute solutions, but I'd consider Spark first
> due to the widespread use and community. I currently have my data loaded
> into Apache Hbase for a different scenario (random access of rows/columns).
> I’ve naively tired loading a dataframe from the CSV using a Spark instance
> hosted on AWS EMR, but getting the results for even a single correlation
> takes over 20 seconds.
>
>
>
> Thank you!
>
>
>
>
>
> --gautham
>
>
>
>
--
*Patrick McCarthy *
Senior Data Scientist, Machine Learning Engineering
Dstillery
470 Park Ave South, 17th Floor, NYC 10016
RE: [Beginner] Run compute on large matrices and return the result in
seconds?
Posted by Gautham Acharya <ga...@alleninstitute.org>.
Thanks for the reply, Bobby.
I’ve received notice that we can probably tolerate response times of up to 30 seconds. Would this be more manageable? 5 seconds was an initial ask, but 20-30 seconds is also a reasonable response time for our use case.
With the new SLA, do you think that we can easily perform this computation in spark?
--gautham
From: Bobby Evans [mailto:revans2@gmail.com]
Sent: Wednesday, July 17, 2019 7:06 AM
To: Steven Stetzler <st...@gmail.com>
Cc: Gautham Acharya <ga...@alleninstitute.org>; user@spark.apache.org
Subject: Re: [Beginner] Run compute on large matrices and return the result in seconds?
CAUTION: This email originated from outside the Allen Institute. Please do not click links or open attachments unless you've validated the sender and know the content is safe.
________________________________
Let's do a few quick rules of thumb to get an idea of what kind of processing power you will need in general to do what you want.
You need 3,000,000 ints by 50,000 rows. Each int is 4 bytes so that ends up being about 560 GB that you need to fully process in 5 seconds.
If you are reading this from spinning disks (which average about 80 MB/s) you would need at least 1,450 disks to just read the data in 5 seconds (that number can vary a lot depending on the storage format and your compression ratio).
If you are reading the data over a network (let's say 10GigE even though in practice you cannot get that in the cloud easily) you would need about 90 NICs just to read the data in 5 seconds, again depending on the compression ration this may be lower.
If you assume you have a cluster where it all fits in main memory and have cached all of the data in memory (which in practice I have seen on most modern systems at somewhere between 12 and 16 GB/sec) you would need between 7 and 10 machines just to read through the data once in 5 seconds. Spark also stores cached data compressed so you might need less as well.
All the numbers fit with things that spark should be able to handle, but a 5 second SLA is very tight for this amount of data.
Can you make this work with Spark? probably. Does spark have something built in that will make this fast and simple for you? I doubt it you have some very tight requirements and will likely have to write something custom to make it work the way you want.
On Thu, Jul 11, 2019 at 4:12 PM Steven Stetzler <st...@gmail.com>> wrote:
Hi Gautham,
I am a beginner spark user too and I may not have a complete understanding of your question, but I thought I would start a discussion anyway. Have you looked into using Spark's built in Correlation function? (https://spark.apache.org/docs/latest/ml-statistics.html<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fspark.apache.org%2Fdocs%2Flatest%2Fml-statistics.html&data=02%7C01%7C%7C7d44353d2dd5420bc35108d70abff11d%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C1%7C636989691818858010&sdata=UG7owx%2FyHayKECNbDbfoNV53nJCSlF06Oak1plpi4RY%3D&reserved=0>) This might let you get what you want (per-row correlation against the same matrix) without having to deal with parallelizing the computation yourself. Also, I think the question of how quick you can get your results is largely a data access question vs how fast is Spark question. As long as you can exploit data parallelism (i.e. you can partition up your data), Spark will give you a speedup. You can imagine that if you had a large machine with many cores and ~100 GB of RAM (e.g. a m5.12xlarge EC2 instance), you could fit your problem in main memory and perform your computation with thread based parallelism. This might get your result relatively quickly. For a dedicated application with well constrained memory and compute requirements, it might not be a bad option to do everything on one machine as well. Accessing an external database and distributing work over a large number of computers can add overhead that might be out of your control.
Thanks,
Steven
On Thu, Jul 11, 2019 at 9:24 AM Gautham Acharya <ga...@alleninstitute.org>> wrote:
Ping? I would really appreciate advice on this! Thank you!
From: Gautham Acharya
Sent: Tuesday, July 9, 2019 4:22 PM
To: user@spark.apache.org<ma...@spark.apache.org>
Subject: [Beginner] Run compute on large matrices and return the result in seconds?
This is my first email to this mailing list, so I apologize if I made any errors.
My team's going to be building an application and I'm investigating some options for distributed compute systems. We want to be performing computes on large matrices.
The requirements are as follows:
1. The matrices can be expected to be up to 50,000 columns x 3 million rows. The values are all integers (except for the row/column headers).
2. The application needs to select a specific row, and calculate the correlation coefficient ( https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.corr.html<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpandas.pydata.org%2Fpandas-docs%2Fstable%2Freference%2Fapi%2Fpandas.DataFrame.corr.html&data=02%7C01%7C%7C7d44353d2dd5420bc35108d70abff11d%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C1%7C636989691818868018&sdata=e5blX8ItE1JDJRx9D3FnmsXp4TnOKvyH6fA6%2Fw2QTbI%3D&reserved=0> ) against every other row. This means up to 3 million different calculations.
3. A sorted list of the correlation coefficients and their corresponding row keys need to be returned in under 5 seconds.
4. Users will eventually request random row/column subsets to run calculations on, so precomputing our coefficients is not an option. This needs to be done on request.
I've been looking at many compute solutions, but I'd consider Spark first due to the widespread use and community. I currently have my data loaded into Apache Hbase for a different scenario (random access of rows/columns). I’ve naively tired loading a dataframe from the CSV using a Spark instance hosted on AWS EMR, but getting the results for even a single correlation takes over 20 seconds.
Thank you!
--gautham
Re: [Beginner] Run compute on large matrices and return the result in seconds?
Posted by Bobby Evans <re...@gmail.com>.
Let's do a few quick rules of thumb to get an idea of what kind of
processing power you will need in general to do what you want.
You need 3,000,000 ints by 50,000 rows. Each int is 4 bytes so that ends
up being about 560 GB that you need to fully process in 5 seconds.
If you are reading this from spinning disks (which average about 80 MB/s)
you would need at least 1,450 disks to just read the data in 5 seconds
(that number can vary a lot depending on the storage format and your
compression ratio).
If you are reading the data over a network (let's say 10GigE even though in
practice you cannot get that in the cloud easily) you would need about 90
NICs just to read the data in 5 seconds, again depending on the compression
ration this may be lower.
If you assume you have a cluster where it all fits in main memory and have
cached all of the data in memory (which in practice I have seen on most
modern systems at somewhere between 12 and 16 GB/sec) you would need
between 7 and 10 machines just to read through the data once in 5 seconds.
Spark also stores cached data compressed so you might need less as well.
All the numbers fit with things that spark should be able to handle, but a
5 second SLA is very tight for this amount of data.
Can you make this work with Spark? probably. Does spark have something
built in that will make this fast and simple for you? I doubt it you have
some very tight requirements and will likely have to write something custom
to make it work the way you want.
On Thu, Jul 11, 2019 at 4:12 PM Steven Stetzler <st...@gmail.com>
wrote:
> Hi Gautham,
>
> I am a beginner spark user too and I may not have a complete understanding
> of your question, but I thought I would start a discussion anyway. Have you
> looked into using Spark's built in Correlation function? (
> https://spark.apache.org/docs/latest/ml-statistics.html) This might let
> you get what you want (per-row correlation against the same matrix) without
> having to deal with parallelizing the computation yourself. Also, I think
> the question of how quick you can get your results is largely a data access
> question vs how fast is Spark question. As long as you can exploit data
> parallelism (i.e. you can partition up your data), Spark will give you a
> speedup. You can imagine that if you had a large machine with many cores
> and ~100 GB of RAM (e.g. a m5.12xlarge EC2 instance), you could fit your
> problem in main memory and perform your computation with thread based
> parallelism. This might get your result relatively quickly. For a dedicated
> application with well constrained memory and compute requirements, it might
> not be a bad option to do everything on one machine as well. Accessing an
> external database and distributing work over a large number of computers
> can add overhead that might be out of your control.
>
> Thanks,
> Steven
>
> On Thu, Jul 11, 2019 at 9:24 AM Gautham Acharya <
> gauthama@alleninstitute.org> wrote:
>
>> Ping? I would really appreciate advice on this! Thank you!
>>
>>
>>
>> *From:* Gautham Acharya
>> *Sent:* Tuesday, July 9, 2019 4:22 PM
>> *To:* user@spark.apache.org
>> *Subject:* [Beginner] Run compute on large matrices and return the
>> result in seconds?
>>
>>
>>
>> This is my first email to this mailing list, so I apologize if I made any
>> errors.
>>
>>
>>
>> My team's going to be building an application and I'm investigating some
>> options for distributed compute systems. We want to be performing computes
>> on large matrices.
>>
>>
>>
>> The requirements are as follows:
>>
>>
>>
>> 1. The matrices can be expected to be up to 50,000 columns x 3
>> million rows. The values are all integers (except for the row/column
>> headers).
>>
>> 2. The application needs to select a specific row, and calculate the
>> correlation coefficient (
>> https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.corr.html )
>> against every other row. This means up to 3 million different calculations.
>>
>> 3. A sorted list of the correlation coefficients and their
>> corresponding row keys need to be returned in under 5 seconds.
>>
>> 4. Users will eventually request random row/column subsets to run
>> calculations on, so precomputing our coefficients is not an option. This
>> needs to be done on request.
>>
>>
>>
>> I've been looking at many compute solutions, but I'd consider Spark first
>> due to the widespread use and community. I currently have my data loaded
>> into Apache Hbase for a different scenario (random access of rows/columns).
>> I’ve naively tired loading a dataframe from the CSV using a Spark instance
>> hosted on AWS EMR, but getting the results for even a single correlation
>> takes over 20 seconds.
>>
>>
>>
>> Thank you!
>>
>>
>>
>>
>>
>> --gautham
>>
>>
>>
>
Re: [Beginner] Run compute on large matrices and return the result in seconds?
Posted by Steven Stetzler <st...@gmail.com>.
Hi Gautham,
I am a beginner spark user too and I may not have a complete understanding
of your question, but I thought I would start a discussion anyway. Have you
looked into using Spark's built in Correlation function? (
https://spark.apache.org/docs/latest/ml-statistics.html) This might let you
get what you want (per-row correlation against the same matrix) without
having to deal with parallelizing the computation yourself. Also, I think
the question of how quick you can get your results is largely a data access
question vs how fast is Spark question. As long as you can exploit data
parallelism (i.e. you can partition up your data), Spark will give you a
speedup. You can imagine that if you had a large machine with many cores
and ~100 GB of RAM (e.g. a m5.12xlarge EC2 instance), you could fit your
problem in main memory and perform your computation with thread based
parallelism. This might get your result relatively quickly. For a dedicated
application with well constrained memory and compute requirements, it might
not be a bad option to do everything on one machine as well. Accessing an
external database and distributing work over a large number of computers
can add overhead that might be out of your control.
Thanks,
Steven
On Thu, Jul 11, 2019 at 9:24 AM Gautham Acharya <ga...@alleninstitute.org>
wrote:
> Ping? I would really appreciate advice on this! Thank you!
>
>
>
> *From:* Gautham Acharya
> *Sent:* Tuesday, July 9, 2019 4:22 PM
> *To:* user@spark.apache.org
> *Subject:* [Beginner] Run compute on large matrices and return the result
> in seconds?
>
>
>
> This is my first email to this mailing list, so I apologize if I made any
> errors.
>
>
>
> My team's going to be building an application and I'm investigating some
> options for distributed compute systems. We want to be performing computes
> on large matrices.
>
>
>
> The requirements are as follows:
>
>
>
> 1. The matrices can be expected to be up to 50,000 columns x 3
> million rows. The values are all integers (except for the row/column
> headers).
>
> 2. The application needs to select a specific row, and calculate the
> correlation coefficient (
> https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.corr.html )
> against every other row. This means up to 3 million different calculations.
>
> 3. A sorted list of the correlation coefficients and their
> corresponding row keys need to be returned in under 5 seconds.
>
> 4. Users will eventually request random row/column subsets to run
> calculations on, so precomputing our coefficients is not an option. This
> needs to be done on request.
>
>
>
> I've been looking at many compute solutions, but I'd consider Spark first
> due to the widespread use and community. I currently have my data loaded
> into Apache Hbase for a different scenario (random access of rows/columns).
> I’ve naively tired loading a dataframe from the CSV using a Spark instance
> hosted on AWS EMR, but getting the results for even a single correlation
> takes over 20 seconds.
>
>
>
> Thank you!
>
>
>
>
>
> --gautham
>
>
>
RE: [Beginner] Run compute on large matrices and return the result in
seconds?
Posted by Gautham Acharya <ga...@alleninstitute.org>.
Ping? I would really appreciate advice on this! Thank you!
From: Gautham Acharya
Sent: Tuesday, July 9, 2019 4:22 PM
To: user@spark.apache.org
Subject: [Beginner] Run compute on large matrices and return the result in seconds?
This is my first email to this mailing list, so I apologize if I made any errors.
My team's going to be building an application and I'm investigating some options for distributed compute systems. We want to be performing computes on large matrices.
The requirements are as follows:
1. The matrices can be expected to be up to 50,000 columns x 3 million rows. The values are all integers (except for the row/column headers).
2. The application needs to select a specific row, and calculate the correlation coefficient ( https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.corr.html ) against every other row. This means up to 3 million different calculations.
3. A sorted list of the correlation coefficients and their corresponding row keys need to be returned in under 5 seconds.
4. Users will eventually request random row/column subsets to run calculations on, so precomputing our coefficients is not an option. This needs to be done on request.
I've been looking at many compute solutions, but I'd consider Spark first due to the widespread use and community. I currently have my data loaded into Apache Hbase for a different scenario (random access of rows/columns). I've naively tired loading a dataframe from the CSV using a Spark instance hosted on AWS EMR, but getting the results for even a single correlation takes over 20 seconds.
Thank you!
--gautham