Re: [spctools-discuss] Multi core analysis

[Jimmy Eng]

If you're running low-res searches (i.e. fragment_bin_size = 1.0005) then
you can probably afford to set this value even higher.  Just try starting a
search and keeping an eye on memory use.  As soon as each batch of spectra
is loaded and being searched against the sequence database, that should be
approximately the maximum amount of memory that Comet will be using.  So
you want to set the batch size as big as possible without running out of
memory, say shoot for 80% to 90% memory use.  The larger the batch size,
the more efficient the search is because it reduces some redundant
calculations.  At some point, the performance gains do level off.

Figure 3 of the manuscript "A deeper look into Comet--implementation and
features."  shows the trade off between batch size, memory use and run
times:

http://link.springer.com/article/10.1007%2Fs13361-015-1179-x






On Wed, Aug 10, 2016 at 1:02 PM, Eslam Nouri  wrote:

> Hi Jimmy,
>
> Thanks a lot for the recommendation. I changed the spectra batch size from
> 1000 to 5000 and could analyze the same DDA sample with 50% improvement in
> the analysis time. I will surely check the 1 spectra batch size to see
> if I can obtain shorter analysis time.
>
> Thanks, Eslam
>
> On Wed, Aug 10, 2016 at 7:54 AM, Jimmy Eng  wrote:
>
>> How much memory/RAM do you have on your computer?  It won't make a huge
>> difference but larger spectrum batch sizes are more efficient.  So see if
>> you have enough free memory to run with that parameter set at say 5000.
>> With our 16GB linux computers performing  high-res ms/ms searches, I use
>> batch sizes of 1.
>>
>> On Wed, Aug 10, 2016 at 12:27 AM, Eslam Nouri 
>> wrote:
>>
>>> Thanks a lot Jimmy. It is a relief to know that I am doing the best that
>>> I can do with my current system.
>>>
>>> I have already removed all the dynamic modifications that I had (no
>>> methionine oxidation or phosphorylations were defined). I have also
>>> confined the analysis to 1000 spectra batch size. Database search takes a
>>> long time, but it identifies a large number of microbiome proteins with
>>> high confidence.
>>>
>>> Eslam
>>>
>>> On Tue, Aug 9, 2016 at 11:39 PM, Jimmy Eng  wrote:
>>>
 Eslam,

 Setting "num_threads = 0" is the best you can do.  There's no free
 lunch ... a database that's 100 times larger than the human UniProt fasta
 will take approximately 100 times longer to run, e.g. a 10 minute human
 search would translate to a 17 hour search if the database were 100 times
 larger.  You can give things up (no variable modifications, no missed
 cleavages, narrow precursor mass tolerance, etc.) to hopefully speed things
 up a little bit.  Otherwise you just have to throw more horsepower at it.
 You can get Broadwell-class Xeon processors with up to 24 cores in them.

 On Tue, Aug 9, 2016 at 11:30 PM, Eslam Nouri 
 wrote:

> Hi Eric,
>
> I am using comet. In my comet file the number of threads is equal to
> zero "num_threads = 0". I have attached my system information. Is
> there any way to increase the data analysis time by defining a thread
> number?
>
> Thanks, Eslam
>
> On Tue, Aug 9, 2016 at 11:18 PM, Eric Deutsch <
> edeut...@systemsbiology.org> wrote:
>
>> Which search engine are you using? Comet? Tandem?
>>
>>
>>
>> Comet has num_threads:
>>
>> http://comet-ms.sourceforge.net/parameters/parameters_201601
>> /num_threads.php
>>
>>
>>
>> Tandem has threads:
>>
>> http://www.thegpm.org/TANDEM/api/st.html
>>
>>
>>
>>
>>
>>
>>
>> *From:* spctools-discuss@googlegroups.com [mailto:
>> spctools-discuss@googlegroups.com] *On Behalf Of *Eslam Nouri
>> *Sent:* Tuesday, August 9, 2016 11:05 PM
>> *To:* spctools-discuss@googlegroups.com
>> *Subject:* [spctools-discuss] Multi core analysis
>>
>>
>>
>> Hello_
>>
>>
>>
>> I am using TPP for the database search of microbiome proteins. Since
>> the fasta file that I have is more than 100 times larger than human 
>> uniprot
>> fasta file, the database search for a single DDA run takes more than 12
>> hours. Is there any way to have faster analysis using multi-cores?
>>
>>
>>
>> Thanks, Eslam
>>
>> Proteomics core facility
>>
>> University of southern California
>>
>> --
>> You received this message because you are subscribed to the Google
>> Groups "spctools-discuss" group.
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>> send an email to spctools-discuss+unsubscr...@googlegroups.com.
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>> com.
>> Visit this group at https://groups.google.com/group/spctools-discuss.
>> For more 

Re: [spctools-discuss] Multi core analysis

[Eslam Nouri]

Hi Jimmy,

Thanks a lot for the recommendation. I changed the spectra batch size from
1000 to 5000 and could analyze the same DDA sample with 50% improvement in
the analysis time. I will surely check the 1 spectra batch size to see
if I can obtain shorter analysis time.

Thanks, Eslam

On Wed, Aug 10, 2016 at 7:54 AM, Jimmy Eng  wrote:

> How much memory/RAM do you have on your computer?  It won't make a huge
> difference but larger spectrum batch sizes are more efficient.  So see if
> you have enough free memory to run with that parameter set at say 5000.
> With our 16GB linux computers performing  high-res ms/ms searches, I use
> batch sizes of 1.
>
> On Wed, Aug 10, 2016 at 12:27 AM, Eslam Nouri 
> wrote:
>
>> Thanks a lot Jimmy. It is a relief to know that I am doing the best that
>> I can do with my current system.
>>
>> I have already removed all the dynamic modifications that I had (no
>> methionine oxidation or phosphorylations were defined). I have also
>> confined the analysis to 1000 spectra batch size. Database search takes a
>> long time, but it identifies a large number of microbiome proteins with
>> high confidence.
>>
>> Eslam
>>
>> On Tue, Aug 9, 2016 at 11:39 PM, Jimmy Eng  wrote:
>>
>>> Eslam,
>>>
>>> Setting "num_threads = 0" is the best you can do.  There's no free lunch
>>> ... a database that's 100 times larger than the human UniProt fasta will
>>> take approximately 100 times longer to run, e.g. a 10 minute human search
>>> would translate to a 17 hour search if the database were 100 times larger.
>>> You can give things up (no variable modifications, no missed cleavages,
>>> narrow precursor mass tolerance, etc.) to hopefully speed things up a
>>> little bit.  Otherwise you just have to throw more horsepower at it.  You
>>> can get Broadwell-class Xeon processors with up to 24 cores in them.
>>>
>>> On Tue, Aug 9, 2016 at 11:30 PM, Eslam Nouri 
>>> wrote:
>>>
 Hi Eric,

 I am using comet. In my comet file the number of threads is equal to
 zero "num_threads = 0". I have attached my system information. Is
 there any way to increase the data analysis time by defining a thread
 number?

 Thanks, Eslam

 On Tue, Aug 9, 2016 at 11:18 PM, Eric Deutsch <
 edeut...@systemsbiology.org> wrote:

> Which search engine are you using? Comet? Tandem?
>
>
>
> Comet has num_threads:
>
> http://comet-ms.sourceforge.net/parameters/parameters_201601
> /num_threads.php
>
>
>
> Tandem has threads:
>
> http://www.thegpm.org/TANDEM/api/st.html
>
>
>
>
>
>
>
> *From:* spctools-discuss@googlegroups.com [mailto:
> spctools-discuss@googlegroups.com] *On Behalf Of *Eslam Nouri
> *Sent:* Tuesday, August 9, 2016 11:05 PM
> *To:* spctools-discuss@googlegroups.com
> *Subject:* [spctools-discuss] Multi core analysis
>
>
>
> Hello_
>
>
>
> I am using TPP for the database search of microbiome proteins. Since
> the fasta file that I have is more than 100 times larger than human 
> uniprot
> fasta file, the database search for a single DDA run takes more than 12
> hours. Is there any way to have faster analysis using multi-cores?
>
>
>
> Thanks, Eslam
>
> Proteomics core facility
>
> University of southern California
>
> --
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> Groups "spctools-discuss" group.
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> For more options, visit https://groups.google.com/d/optout.
>
> --
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RE: [spctools-discuss] pepXML: aminoacid_modification elements in search_summary

[Michael Hoopmann]

I don’t require them in my software that reads pepXML because I don’t find 
these tags reliable, specifically in cases where they are missing. Like 
SpectraST, Kojak doesn’t export these either.

Cheers,

Mike

 

From: spctools-discuss@googlegroups.com 
[mailto:spctools-discuss@googlegroups.com] On Behalf Of Eric Deutsch
Sent: Wednesday, August 10, 2016 12:43 PM
To: spctools-discuss@googlegroups.com
Cc: Eric Deutsch
Subject: [spctools-discuss] pepXML: aminoacid_modification elements in 
search_summary

 

Hi everyone, I have a question about use of some pepXML tags. It’s a bit 
technical and mostly for other developers who use the pepXML format.

 

The issue involves the amino_acid tags at the top of a pepXML file under 
search_summary, like this:



  

  

 

Comet and some other search engines write out these entries for the specified 
search mass mod parameters.

 

But SpectraST at least does not put these there, in part because it doesn’t 
really know what mods will appear in later in the file, because it depends on 
the library. And we now have another case where it is awkward to put them at 
the top of the file because they’re not an input parameter, but a result of the 
reference.

 

So the question to all is: does anyone use these data elements at the top for 
something important? Would it cause any troubles if for some search results 
they are not there or are incomplete? As currently for SpectraST?

 

What do you think?

 

Thanks,

Eric

 

 

 

 

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[spctools-discuss] pepXML: aminoacid_modification elements in search_summary

[Eric Deutsch]

Hi everyone, I have a question about use of some pepXML tags. It’s a bit
technical and mostly for other developers who use the pepXML format.



The issue involves the amino_acid tags at the top of a pepXML file under
search_summary, like this:



  

  



Comet and some other search engines write out these entries for the
specified search mass mod parameters.



But SpectraST at least does not put these there, in part because it doesn’t
really know what mods will appear in later in the file, because it depends
on the library. And we now have another case where it is awkward to put
them at the top of the file because they’re not an input parameter, but a
result of the reference.



So the question to all is: does anyone use these data elements at the top
for something important? Would it cause any troubles if for some search
results they are not there or are incomplete? As currently for SpectraST?



What do you think?



Thanks,

Eric

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Re: [spctools-discuss] Multi core analysis

[Brian Hampton]

Hi Eslam,

Along the lines of what Jimmy mentioned about "giving things up" specifying
fully versus partial tryptic really speeds up the search if that is
suitable for your sample.

I would recommend talking to your IT department to see if they have any
ready solutions for increasing your computing power.  They may have
resources available that you are not aware of.  For example, I talked to
the IT Dept. here and they happily set up a 12 core virtual machine that I
installed TPP on.  They would have done more, but ultimately they wanted to
charge me a yearly fee and I decided to go the less expensive route and buy
pre-owned "pizza boxes" with dual hex cores, install Ubuntu and TPP
myself.  These are relatively inexpensive on E-Bay for ~$500 depending on
configuration.  Here is one example:
http://www.ebay.com/itm/HP-Proliant-DL360-G7-Server-2x-X5670-2-93GHz-HexaCore-128GB-4x-450GB-2x-power-/322197730383?hash=item4b047b344f:g:FOAAAOSwtnpXpQMR
You may be able to work with such companies that sell these units to have
them configured to your specs.

So the above would be for just one shared memory system with 12 cores (+12
virtual cores if you config it that way since these processors support
hyper theading, which may or may not speed things up.  Apparently with
hyper threading more isn't always better).  Using Ubuntu or other Linux
distros, you can set up a cluster of many of these inexpensive boxes that
will work in parallel to further increase your processing power.  With 5
such boxes,  mentioned above, you could have a 60 core cluster for less
than $3000 in hardware.

Ultimately its your budget and ability to do things yourself that will
determine what is best for you.

Cheers,
Brian


Brian Hampton
Protein Analysis Lab
Center for Vascular and Inflammatory Diseases
University of Maryland School of Medicine
655 West Baltimore Street BRB 7-018
Baltimore  MD  21201
V: 410-706-8207


On Wed, Aug 10, 2016 at 2:05 AM, Eslam Nouri  wrote:

> Hello_
>
>
>
> I am using TPP for the database search of microbiome proteins. Since the
> fasta file that I have is more than 100 times larger than human uniprot
> fasta file, the database search for a single DDA run takes more than 12
> hours. Is there any way to have faster analysis using multi-cores?
>
>
>
> Thanks, Eslam
>
> Proteomics core facility
>
> University of southern California
>
> --
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> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
> To post to this group, send email to spctools-discuss@googlegroups.com.
> Visit this group at https://groups.google.com/group/spctools-discuss.
> For more options, visit https://groups.google.com/d/optout.
>

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Re: [spctools-discuss] Multi core analysis

[Jimmy Eng]

How much memory/RAM do you have on your computer?  It won't make a huge
difference but larger spectrum batch sizes are more efficient.  So see if
you have enough free memory to run with that parameter set at say 5000.
With our 16GB linux computers performing  high-res ms/ms searches, I use
batch sizes of 1.

On Wed, Aug 10, 2016 at 12:27 AM, Eslam Nouri  wrote:

> Thanks a lot Jimmy. It is a relief to know that I am doing the best that I
> can do with my current system.
>
> I have already removed all the dynamic modifications that I had (no
> methionine oxidation or phosphorylations were defined). I have also
> confined the analysis to 1000 spectra batch size. Database search takes a
> long time, but it identifies a large number of microbiome proteins with
> high confidence.
>
> Eslam
>
> On Tue, Aug 9, 2016 at 11:39 PM, Jimmy Eng  wrote:
>
>> Eslam,
>>
>> Setting "num_threads = 0" is the best you can do.  There's no free lunch
>> ... a database that's 100 times larger than the human UniProt fasta will
>> take approximately 100 times longer to run, e.g. a 10 minute human search
>> would translate to a 17 hour search if the database were 100 times larger.
>> You can give things up (no variable modifications, no missed cleavages,
>> narrow precursor mass tolerance, etc.) to hopefully speed things up a
>> little bit.  Otherwise you just have to throw more horsepower at it.  You
>> can get Broadwell-class Xeon processors with up to 24 cores in them.
>>
>> On Tue, Aug 9, 2016 at 11:30 PM, Eslam Nouri 
>> wrote:
>>
>>> Hi Eric,
>>>
>>> I am using comet. In my comet file the number of threads is equal to
>>> zero "num_threads = 0". I have attached my system information. Is there
>>> any way to increase the data analysis time by defining a thread number?
>>>
>>> Thanks, Eslam
>>>
>>> On Tue, Aug 9, 2016 at 11:18 PM, Eric Deutsch <
>>> edeut...@systemsbiology.org> wrote:
>>>
 Which search engine are you using? Comet? Tandem?



 Comet has num_threads:

 http://comet-ms.sourceforge.net/parameters/parameters_201601
 /num_threads.php



 Tandem has threads:

 http://www.thegpm.org/TANDEM/api/st.html







 *From:* spctools-discuss@googlegroups.com [mailto:
 spctools-discuss@googlegroups.com] *On Behalf Of *Eslam Nouri
 *Sent:* Tuesday, August 9, 2016 11:05 PM
 *To:* spctools-discuss@googlegroups.com
 *Subject:* [spctools-discuss] Multi core analysis



 Hello_



 I am using TPP for the database search of microbiome proteins. Since
 the fasta file that I have is more than 100 times larger than human uniprot
 fasta file, the database search for a single DDA run takes more than 12
 hours. Is there any way to have faster analysis using multi-cores?



 Thanks, Eslam

 Proteomics core facility

 University of southern California

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>>>
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Re: [spctools-discuss] Multi core analysis

[Eslam Nouri]

Thanks a lot Jimmy. It is a relief to know that I am doing the best that I
can do with my current system.

I have already removed all the dynamic modifications that I had (no
methionine oxidation or phosphorylations were defined). I have also
confined the analysis to 1000 spectra batch size. Database search takes a
long time, but it identifies a large number of microbiome proteins with
high confidence.

Eslam

On Tue, Aug 9, 2016 at 11:39 PM, Jimmy Eng  wrote:

> Eslam,
>
> Setting "num_threads = 0" is the best you can do.  There's no free lunch
> ... a database that's 100 times larger than the human UniProt fasta will
> take approximately 100 times longer to run, e.g. a 10 minute human search
> would translate to a 17 hour search if the database were 100 times larger.
> You can give things up (no variable modifications, no missed cleavages,
> narrow precursor mass tolerance, etc.) to hopefully speed things up a
> little bit.  Otherwise you just have to throw more horsepower at it.  You
> can get Broadwell-class Xeon processors with up to 24 cores in them.
>
> On Tue, Aug 9, 2016 at 11:30 PM, Eslam Nouri  wrote:
>
>> Hi Eric,
>>
>> I am using comet. In my comet file the number of threads is equal to zero
>> "num_threads = 0". I have attached my system information. Is there any
>> way to increase the data analysis time by defining a thread number?
>>
>> Thanks, Eslam
>>
>> On Tue, Aug 9, 2016 at 11:18 PM, Eric Deutsch <
>> edeut...@systemsbiology.org> wrote:
>>
>>> Which search engine are you using? Comet? Tandem?
>>>
>>>
>>>
>>> Comet has num_threads:
>>>
>>> http://comet-ms.sourceforge.net/parameters/parameters_201601
>>> /num_threads.php
>>>
>>>
>>>
>>> Tandem has threads:
>>>
>>> http://www.thegpm.org/TANDEM/api/st.html
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *From:* spctools-discuss@googlegroups.com [mailto:spctools-discuss@googl
>>> egroups.com] *On Behalf Of *Eslam Nouri
>>> *Sent:* Tuesday, August 9, 2016 11:05 PM
>>> *To:* spctools-discuss@googlegroups.com
>>> *Subject:* [spctools-discuss] Multi core analysis
>>>
>>>
>>>
>>> Hello_
>>>
>>>
>>>
>>> I am using TPP for the database search of microbiome proteins. Since the
>>> fasta file that I have is more than 100 times larger than human uniprot
>>> fasta file, the database search for a single DDA run takes more than 12
>>> hours. Is there any way to have faster analysis using multi-cores?
>>>
>>>
>>>
>>> Thanks, Eslam
>>>
>>> Proteomics core facility
>>>
>>> University of southern California
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
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>>>
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>>
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Re: [spctools-discuss] Multi core analysis

[Jimmy Eng]

Eslam,

Setting "num_threads = 0" is the best you can do.  There's no free lunch
... a database that's 100 times larger than the human UniProt fasta will
take approximately 100 times longer to run, e.g. a 10 minute human search
would translate to a 17 hour search if the database were 100 times larger.
You can give things up (no variable modifications, no missed cleavages,
narrow precursor mass tolerance, etc.) to hopefully speed things up a
little bit.  Otherwise you just have to throw more horsepower at it.  You
can get Broadwell-class Xeon processors with up to 24 cores in them.

On Tue, Aug 9, 2016 at 11:30 PM, Eslam Nouri  wrote:

> Hi Eric,
>
> I am using comet. In my comet file the number of threads is equal to zero 
> "num_threads
> = 0". I have attached my system information. Is there any way to increase
> the data analysis time by defining a thread number?
>
> Thanks, Eslam
>
> On Tue, Aug 9, 2016 at 11:18 PM, Eric Deutsch  > wrote:
>
>> Which search engine are you using? Comet? Tandem?
>>
>>
>>
>> Comet has num_threads:
>>
>> http://comet-ms.sourceforge.net/parameters/parameters_201601
>> /num_threads.php
>>
>>
>>
>> Tandem has threads:
>>
>> http://www.thegpm.org/TANDEM/api/st.html
>>
>>
>>
>>
>>
>>
>>
>> *From:* spctools-discuss@googlegroups.com [mailto:spctools-discuss@googl
>> egroups.com] *On Behalf Of *Eslam Nouri
>> *Sent:* Tuesday, August 9, 2016 11:05 PM
>> *To:* spctools-discuss@googlegroups.com
>> *Subject:* [spctools-discuss] Multi core analysis
>>
>>
>>
>> Hello_
>>
>>
>>
>> I am using TPP for the database search of microbiome proteins. Since the
>> fasta file that I have is more than 100 times larger than human uniprot
>> fasta file, the database search for a single DDA run takes more than 12
>> hours. Is there any way to have faster analysis using multi-cores?
>>
>>
>>
>> Thanks, Eslam
>>
>> Proteomics core facility
>>
>> University of southern California
>>
>> --
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>
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RE: [spctools-discuss] Multi core analysis

[Eric Deutsch]

Which search engine are you using? Comet? Tandem?



Comet has num_threads:

http://comet-ms.sourceforge.net/parameters/parameters_201601/num_threads.php



Tandem has threads:

http://www.thegpm.org/TANDEM/api/st.html







*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Eslam Nouri
*Sent:* Tuesday, August 9, 2016 11:05 PM
*To:* spctools-discuss@googlegroups.com
*Subject:* [spctools-discuss] Multi core analysis



Hello_



I am using TPP for the database search of microbiome proteins. Since the
fasta file that I have is more than 100 times larger than human uniprot
fasta file, the database search for a single DDA run takes more than 12
hours. Is there any way to have faster analysis using multi-cores?



Thanks, Eslam

Proteomics core facility

University of southern California

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