[gmx-users] the job is not being distributed
Hi Carsten, Thanks for your reply from where i have got the clue to solve it. Something was wrong with my command and hostfile. Regards Syed Tarique Moin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the job is not being distributed
- Original Message - From: Syed Tarique Moin Date: Thursday, July 1, 2010 4:22 Subject: [gmx-users] the job is not being distributed To: gmx-users@gromacs.org --- | > Hello, > > I have successfully compiled gromacs with openmpi but i see the same problem > that the jobs is still not distributed to other nodes but showing all the > processor in node and it should be distributed. | --- We can't help you without you providing a lot more detail. Be sure that you can run other parallel programs and have followed the MPI installation instructions on the GROMACS website. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the job is not being distributed
Hi Syed, you have to give more information for other people to be able to understand what you are doing. What is the exact sequence of commands you use to start the mdrun job? How does your OpenMPI hostfile look like, how are your nodes called, what does mdrun print on the first lines. Without that information, nobody can help you because there is no chance to tell what is possibly going wrong. Carsten On Jun 30, 2010, at 8:21 PM, Syed Tarique Moin wrote: > Hello, > > I have successfully compiled gromacs with openmpi but i see the same problem > that the jobs is still not distributed to other nodes but showing all the > processor in node and it should be distributed. > > Thanks and regards > > Syed Tarique Moin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the job is not being distributed
Hello, I have successfully compiled gromacs with openmpi but i see the same problem that the jobs is still not distributed to other nodes but showing all the processor in node and it should be distributed. Thanks and regards Syed Tarique Moin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the job is not being distributed
Hi, Thanks a lot, i will try openmpi. Regards Syed Tarique Moin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the job is not being distributed
MPICH is known to have problems with GROMACS under at least some circumstances. Try OpenMPI Mark - Original Message - From: Syed Tarique Moin Date: Wednesday, June 30, 2010 22:36 Subject: [gmx-users] the job is not being distributed To: gmx-users@gromacs.org --- | > Hi, > > Thanks but the with AMBER its working. If it had been the problem of cluster. > It should be with AMBER too. > > Regards > > Syed Tarique Moin > | --- > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the job is not being distributed
Hi, Thanks but the with AMBER its working. If it had been the problem of cluster. It should be with AMBER too. Regards Syed Tarique Moin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the job is not being distributed
I think this is not a problem of Gromacs, but the cluster you are using. Try to contact with your cluster administrator, and check the administration software. Syed Tarique Moin wrote: > Hi, > > I am using MPICH2 library for gromacs. > > Thanks and Regards > > Syed Tarique Moin > > > > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the job is not being distributed
Hi, I am using MPICH2 library for gromacs. Thanks and Regards Syed Tarique Moin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the job is not being distributed
So which MPI library are you using? Carsten On Jun 28, 2010, at 3:33 PM, Syed Tarique Moin wrote: > Hi, > > In case Amber simulation, i run command of mpirun and the jobs are > distributed into different nodes 4 on each machines but in case i am > observing that all the 8 processes are on node01 but no indication on node02 > unlike in case of amber. > > Thanks > > Syed Tarique Moin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the job is not being distributed
Hi, In case Amber simulation, i run command of mpirun and the jobs are distributed into different nodes 4 on each machines but in case i am observing that all the 8 processes are on node01 but no indication on node02 unlike in case of amber. Thanks Syed Tarique Moin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the job is not being distributed
On Jun 28, 2010, at 2:34 PM, Syed Tarique Moin wrote: > hello, > > I am running a simulation on dual core processor using the following command > > mpirun -np 8 mdrun_mpi -s top > > The job is running but it is not distributed on other node, i mean i cant see > the process on other nodes as well. I see only on node01 but it has only 4 > processors. Can anybody suggest me! > > > Hi, find out how you generally run a simple parallel job with the MPI framework that you are using. If that works, Gromacs should also run in parallel. You are going to have to provide some kind of machine / host / nodefile. Carsten -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the job is not being distributed
hello, I am running a simulation on dual core processor using the following command mpirun -np 8 mdrun_mpi -s top The job is running but it is not distributed on other node, i mean i cant see the process on other nodes as well. I see only on node01 but it has only 4 processors. Can anybody suggest me! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
