[ccp4bb] SHELXD - Limit Number of CPUs?

[Isabel Uson]

Hi Jessica,

there is a flag -t, which you should give in the command line to set the
number of threads. eg shelxd -t4 name

Best wishes,

Isabel

-- 
ICREA Res. Prof. Isabel Usón
Crystallographic Methods
Department of Structural Biology (“Maria de Maeztu” 2014 Unit of Excellence),

Molecular Biology Institute of Barcelona, Spanish Research Council;
Barcelona Science Park, Helix Building, 08028 Barcelona (Spain)
http://chango.ibmb.csic.es/ARCIMBOLDO



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] SHELXD - Limit Number of CPUs?

[Jessica Bruhn]

Hi all,

Thank you for the excellent advice. I think I have found what I am looking
for.

To James, I am currently not using a queuing system and I am just launching
jobs directly on a shared GPU machine. Soon I will move to a PBS cluster,
which should help with all of this.

Thanks again!

Cheers,
Jessica

On Wed, Mar 16, 2022 at 10:26 PM Tim Gruene  wrote:

> Hi Jessica,
>
> like most shelx programs, there is a little help message when started
> without command line options. The option
>
> '-tN' sets the number of CPUs to N. If I remember correctly, SHELXD
> also respects the environment variable OMP_NUM_THREADS.
>
> Best,
> Tim
>
> On Wed, 16 Mar 2022 17:21:38 -0700 Jessica Bruhn
> <450e5de75376-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> > Hi all,
> >
> > I am wondering if there is a way to limit the number of CPUs that can
> > be used by SHELXD. It seems that this program uses all that are
> > available until it hits the NTRY you specified or it finds a .fin
> > file. Is there a way to limit its CPU and MEM usage? I am running
> > this on a large cluster along with other jobs and don't want to get
> > myself into trouble.
> >
> > Thanks so much!
> >
> > Best,
> > Jessica
> >
>
>
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>


-- 
Jessica Bruhn, Ph.D
Scientific Group Leader, MicroED
NanoImaging Services, Inc.
4940 Carroll Canyon Road, Suite 115
San Diego, CA 92121
Phone #: (888) 675-8261
www.nanoimagingservices.com



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Re: [ccp4bb] SHELXD - Limit Number of CPUs?

[Tim Gruene]

Hi Jessica,

like most shelx programs, there is a little help message when started
without command line options. The option

'-tN' sets the number of CPUs to N. If I remember correctly, SHELXD
also respects the environment variable OMP_NUM_THREADS.

Best,
Tim

On Wed, 16 Mar 2022 17:21:38 -0700 Jessica Bruhn
<450e5de75376-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi all,
> 
> I am wondering if there is a way to limit the number of CPUs that can
> be used by SHELXD. It seems that this program uses all that are
> available until it hits the NTRY you specified or it finds a .fin
> file. Is there a way to limit its CPU and MEM usage? I am running
> this on a large cluster along with other jobs and don't want to get
> myself into trouble.
> 
> Thanks so much!
> 
> Best,
> Jessica
> 



-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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pgpDOEVyL2SGP.pgp
Description: OpenPGP digital signature

Re: [ccp4bb] SHELXD - Limit Number of CPUs?

[James Holton]

Most cluster queueing systems have a way to limit such things. Which one 
are you using?


You can also set the environment variable OMP_NUM_THREADS to tell SHELXD 
to limit its CPU usage.  You do this with either:

setenv OMP_NUM_THREADS 10
or
export OMP_NUM_THREADS=10

on the command line before running shelxd.

-James Holton
MAD Scientist

On 3/16/2022 5:21 PM, Jessica Bruhn wrote:

Hi all,

I am wondering if there is a way to limit the number of CPUs that can 
be used by SHELXD. It seems that this program uses all that are 
available until it hits the NTRY you specified or it finds a .fin 
file. Is there a way to limit its CPU and MEM usage? I am running this 
on a large cluster along with other jobs and don't want to get myself 
into trouble.


Thanks so much!

Best,
Jessica

--
Jessica Bruhn, Ph.D
Scientific Group Leader, MicroED
NanoImaging Services, Inc.
4940 Carroll Canyon Road, Suite 115
San Diego, CA 92121
Phone #: (888) 675-8261
www.nanoimagingservices.com 



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Re: [ccp4bb] SHELXD - Limit Number of CPUs?

[Lazo, Edwin]

Hi Jessica,

You can use the "cpu" flag. Here is an example:

fast_ep cpu=20 sad=fast_dp.mtz ntry=500

In terms of memory usage, I do not know.

I hope this helps.

Best,

Edwin Lazo
Structural Biology,
National Synchrotron Light Source II
Office: 631.344.7247
el...@bnl.gov<mailto:el...@bnl.gov>
[https://www.bnl.gov/assets/global/images/bnl-logo-email-signature.png]<https://www.bnl.gov/>



From: CCP4 bulletin board  on behalf of Jessica Bruhn 
<450e5de75376-dmarc-requ...@jiscmail.ac.uk>
Sent: Wednesday, March 16, 2022 8:21 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] SHELXD - Limit Number of CPUs?

Hi all,

I am wondering if there is a way to limit the number of CPUs that can be used 
by SHELXD. It seems that this program uses all that are available until it hits 
the NTRY you specified or it finds a .fin file. Is there a way to limit its CPU 
and MEM usage? I am running this on a large cluster along with other jobs and 
don't want to get myself into trouble.

Thanks so much!

Best,
Jessica

--
Jessica Bruhn, Ph.D
Scientific Group Leader, MicroED
NanoImaging Services, Inc.
4940 Carroll Canyon Road, Suite 115
San Diego, CA 92121
Phone #: (888) 675-8261
www.nanoimagingservices.com<https://urldefense.com/v3/__http://www.nanoimagingservices.com/__;!!P4SdNyxKAPE!UdEFPHeeAbeEGobOuQAhyMxWBpWTJfrsoAPdHAqqcoKdc-Ao4K5KVmdydXHYFw$>



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[ccp4bb] SHELXD - Limit Number of CPUs?

[Jessica Bruhn]

Hi all,

I am wondering if there is a way to limit the number of CPUs that can be
used by SHELXD. It seems that this program uses all that are available
until it hits the NTRY you specified or it finds a .fin file. Is there a
way to limit its CPU and MEM usage? I am running this on a large cluster
along with other jobs and don't want to get myself into trouble.

Thanks so much!

Best,
Jessica

-- 
Jessica Bruhn, Ph.D
Scientific Group Leader, MicroED
NanoImaging Services, Inc.
4940 Carroll Canyon Road, Suite 115
San Diego, CA 92121
Phone #: (888) 675-8261
www.nanoimagingservices.com



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