[gmx-users] gromacs.org_gmx-users mailing list submissions
Morten Slyngborg
morten at slyngborg.com
Mon Jul 11 17:08:39 CEST 2016
gromacs.org_gmx-users mailing list submissions
> Den 11/07/2016 kl. 17.06 skrev gromacs.org_gmx-users-request at maillist.sys.kth.se:
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> Today's Topics:
>
> 1. Error running MPI: Open MPI does not support recursive calls
> of mpiexec (Benjamin Joseph Coscia)
> 2. Re: Error running MPI: Open MPI does not support recursive
> calls of mpiexec (Mark Abraham)
> 3. Re: Error running MPI: Open MPI does not support recursive
> calls of mpiexec (Mark Abraham)
> 4. Re: command line issue (Mark Abraham)
> 5. Re: command line issue (Florent H?din)
> 6. Re: command line issue (Albert)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 11 Jul 2016 08:52:39 -0600
> From: Benjamin Joseph Coscia <Benjamin.Coscia at colorado.edu>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Error running MPI: Open MPI does not support
> recursive calls of mpiexec
> Message-ID:
> <CAGNWtmtPCU90sQ=gtf4f_vMfEE1qgZmQeahxr+nW51qWBK-G8Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs Users,
>
> I am trying to run Gromacs on the Xsede resource, Bridges. I have been in
> contact with their help desk to try and figure out this issue. It has been
> nearly a month without resolution, so I thought I would see if anyone else
> has had this problem or could offer suggestions on how to fix it.
>
> The problem is that every time I run a job (using this command: mpirun -np
> 28 gmx_mpi mdrun -v -deffnm job), I get the error:
>
> "Open MPI does not support recursive calls of mpiexec"
>
> I've tried running jobs by submitting batch scripts with slurm. I've also
> tried running jobs using interactive nodes. Finally, I've used an example
> batch submission script which is given by the people at Bridges. Even after
> getting help and making sure that I was submitting a scripts that should
> work, I get the same error as above. The most frustrating part is that
> these scripts used to run just fine. When I was doing simulations to get
> scaling data, they ran exactly as I wanted them to. After getting an
> allocation two months later, I tried running the exact same scripts and
> they did not work. I can however, run other MPI programs no problem (simple
> scripts I got from a workshop about MPI).
>
> I read in an earlier thread that there may be issues related to OpenMPI
> version 1.10.0 and the 1.10.3 may be the better option. Do you think that
> suggesting upgrading to version 1.10.3 might help resolve this issue?
>
> Thank you for your help!
> Ben Coscia
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 11 Jul 2016 15:02:21 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, Benjamin.Coscia at colorado.edu,
> gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Error running MPI: Open MPI does not support
> recursive calls of mpiexec
> Message-ID:
> <CAMNuMASDdTCTkeMuhbTFknzqvU9TtbGRR49Sf8uMX3C7S4TbzQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Sorry to hear that. Unfortunately, there's no possibility that mpirun -np
> 28 gmx_mpi mdrun" could trigger that error from a correct MPI installation.
> gmx_mpi tune_pme could do that, but for that to explain your observations
> would require some kind of bizarre dynamic linking problem. Much more
> likely is an issue with the MPI library, though I can't see one fixed in
> the OpenMPI 1.10.x release notes. I would indeed suggest 1.10.3, or the
> latest 1.8.x.
>
> Mark
>
> On Mon, Jul 11, 2016 at 4:52 PM Benjamin Joseph Coscia <
> Benjamin.Coscia at colorado.edu> wrote:
>
>> Dear Gromacs Users,
>>
>> I am trying to run Gromacs on the Xsede resource, Bridges. I have been in
>> contact with their help desk to try and figure out this issue. It has been
>> nearly a month without resolution, so I thought I would see if anyone else
>> has had this problem or could offer suggestions on how to fix it.
>>
>> The problem is that every time I run a job (using this command: mpirun -np
>> 28 gmx_mpi mdrun -v -deffnm job), I get the error:
>>
>> "Open MPI does not support recursive calls of mpiexec"
>>
>> I've tried running jobs by submitting batch scripts with slurm. I've also
>> tried running jobs using interactive nodes. Finally, I've used an example
>> batch submission script which is given by the people at Bridges. Even after
>> getting help and making sure that I was submitting a scripts that should
>> work, I get the same error as above. The most frustrating part is that
>> these scripts used to run just fine. When I was doing simulations to get
>> scaling data, they ran exactly as I wanted them to. After getting an
>> allocation two months later, I tried running the exact same scripts and
>> they did not work. I can however, run other MPI programs no problem (simple
>> scripts I got from a workshop about MPI).
>>
>> I read in an earlier thread that there may be issues related to OpenMPI
>> version 1.10.0 and the 1.10.3 may be the better option. Do you think that
>> suggesting upgrading to version 1.10.3 might help resolve this issue?
>>
>> Thank you for your help!
>> Ben Coscia
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 11 Jul 2016 15:02:21 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, Benjamin.Coscia at colorado.edu,
> gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Error running MPI: Open MPI does not support
> recursive calls of mpiexec
> Message-ID:
> <CAMNuMASDdTCTkeMuhbTFknzqvU9TtbGRR49Sf8uMX3C7S4TbzQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Sorry to hear that. Unfortunately, there's no possibility that mpirun -np
> 28 gmx_mpi mdrun" could trigger that error from a correct MPI installation.
> gmx_mpi tune_pme could do that, but for that to explain your observations
> would require some kind of bizarre dynamic linking problem. Much more
> likely is an issue with the MPI library, though I can't see one fixed in
> the OpenMPI 1.10.x release notes. I would indeed suggest 1.10.3, or the
> latest 1.8.x.
>
> Mark
>
> On Mon, Jul 11, 2016 at 4:52 PM Benjamin Joseph Coscia <
> Benjamin.Coscia at colorado.edu> wrote:
>
>> Dear Gromacs Users,
>>
>> I am trying to run Gromacs on the Xsede resource, Bridges. I have been in
>> contact with their help desk to try and figure out this issue. It has been
>> nearly a month without resolution, so I thought I would see if anyone else
>> has had this problem or could offer suggestions on how to fix it.
>>
>> The problem is that every time I run a job (using this command: mpirun -np
>> 28 gmx_mpi mdrun -v -deffnm job), I get the error:
>>
>> "Open MPI does not support recursive calls of mpiexec"
>>
>> I've tried running jobs by submitting batch scripts with slurm. I've also
>> tried running jobs using interactive nodes. Finally, I've used an example
>> batch submission script which is given by the people at Bridges. Even after
>> getting help and making sure that I was submitting a scripts that should
>> work, I get the same error as above. The most frustrating part is that
>> these scripts used to run just fine. When I was doing simulations to get
>> scaling data, they ran exactly as I wanted them to. After getting an
>> allocation two months later, I tried running the exact same scripts and
>> they did not work. I can however, run other MPI programs no problem (simple
>> scripts I got from a workshop about MPI).
>>
>> I read in an earlier thread that there may be issues related to OpenMPI
>> version 1.10.0 and the 1.10.3 may be the better option. Do you think that
>> suggesting upgrading to version 1.10.3 might help resolve this issue?
>>
>> Thank you for your help!
>> Ben Coscia
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 11 Jul 2016 15:03:35 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] command line issue
> Message-ID:
> <CAMNuMASj9DtyDupyqGCzS8YLzSDxYexXtP+TQiQ3Wx_o+GKcng at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Yes, like I said :-) We asked users some years ago, and there was
> enthusiasm for bash and zsh. Few people encourage the use of the csh family
> these days.
>
> Mark
>
>> On Mon, Jul 11, 2016 at 4:52 PM Albert <mailmd2011 at gmail.com> wrote:
>>
>> Hi:
>>
>> I do add this in my .cshrc:
>>
>> source /home/albert/install/gromacs/5.1.2/bin/GMXRC
>>
>> however, it doesn't work in my tcsh. It seems to work only in Bash.....
>>
>> regards
>>
>>
>>
>>> On 07/11/2016 04:48 PM, Mark Abraham wrote:
>>> Hi,
>>>
>>> If you have used "source GMXRC" from a supported shell (bash and zsh, I
>>> think) then this will work. It also knows about command-line options and
>>> file extensions.
>>>
>>> Mark
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 11 Jul 2016 17:05:07 +0200
> From: Florent H?din <work at fhedin.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] command line issue
> Message-ID: <84f06956-c188-8d6b-edf6-2bfdedd7c693 at fhedin.com>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hi,
> what about using instead the csh file. i.e.
>
> source /home/albert/install/gromacs/5.1.2/bin/GMXRC.csh
>
> there are several versions of the file, for different shells :
>
> -rwxr-xr-x 1 root root 566 Jul 8 11:13 GMXRC
> -rwxr-xr-x 1 root root 2.7K Jul 8 11:13 GMXRC.bash
> -rwxr-xr-x 1 root root 3.0K Jul 8 11:13 GMXRC.csh
> -rwxr-xr-x 1 root root 118 Jul 8 11:13 GMXRC.zsh
>
> Cheers,
>
> Florent
>
>> On 11/07/16 16:51, Albert wrote:
>> Hi:
>>
>> I do add this in my .cshrc:
>>
>> source /home/albert/install/gromacs/5.1.2/bin/GMXRC
>>
>> however, it doesn't work in my tcsh. It seems to work only in Bash.....
>>
>> regards
>>
>>
>>
>>> On 07/11/2016 04:48 PM, Mark Abraham wrote:
>>> Hi,
>>>
>>> If you have used "source GMXRC" from a supported shell (bash and zsh, I
>>> think) then this will work. It also knows about command-line options and
>>> file extensions.
>>>
>>> Mark
>
> --
> <p>
> Florent H?din <br/>
> Department of Chemistry <br/>
> University of Basel <br/>
> Klingelbergstrasse 80 <br/>
> CH-4056 Basel, Switzerland <br/>
> <a
> href="http://www.chemie.unibas.ch/~hedin">http://www.chemie.unibas.ch/~hedin</a><br/>
> </p>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 11 Jul 2016 17:05:59 +0200
> From: Albert <mailmd2011 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] command line issue
> Message-ID: <5783B5D7.6030904 at gmail.com>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> HMMM....but I found that many professional software actually prefer to
> support CSH......
>
> I am just wondering is it possible to make this useful function also
> works in csh?
>
> thx a lot
>
>> On 07/11/2016 05:03 PM, Mark Abraham wrote:
>> Hi,
>>
>> Yes, like I said:-) We asked users some years ago, and there was
>> enthusiasm for bash and zsh. Few people encourage the use of the csh family
>> these days.
>>
>> Mark
>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 147, Issue 58
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