[mvapich-discuss] mvapich and gromacs4.6

[hpc at lzu.edu.cn]

Dear Jiri


    Thanks! the output error is:

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 2

gcq#319: "Your Country Raised You, Your Country Fed You, and Just Like Any Other Country it Will Break You" (Gogol Bordello)

[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0

-------------------------------------------------------
Program mdrun_mpi, VERSION 4.6.3
Source code file: /home/*/gromacs-4.6.3/src/gmxlib/gmx_detect_hardware.c, line: 349

Fatal error:
Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node.
mdrun_mpi was started with 1 PP MPI process per node, but you provided 2 GPUs.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"We Can Dance Like Iggy Pop" (Red Hot Chili Peppers)

Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 2

gcq#5: "We Can Dance Like Iggy Pop" (Red Hot Chili Peppers)

[cli_1]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1


 

-----原始邮件-----
发件人: "Jiri Kraus" <jkraus at nvidia.com>
发送时间: 2013-11-17 11:20:48 (星期日)
收件人: "sreeram potluri" <potluri.2 at osu.edu>, "hpc at lzu.edu.cn" <hpc at lzu.edu.cn>
抄送: mvapich-discuss <mvapich-discuss at cse.ohio-state.edu>
主题: AW: [mvapich-discuss] mvapich and gromacs4.6


Dear Yang,


please also add the output of mdrun. GROMACS supports one GPU per MPI rank so you need to start as many ranks per node as there are GPUs in a node to utilize all GPUs.


Hope this helps


Jiri


Sent from my smartphone, I apologize for spelling errors and auto correction typos.


----- Reply message -----
Von: "sreeram potluri" <potluri.2 at osu.edu>
An: "hpc at lzu.edu.cn" <hpc at lzu.edu.cn>
Cc: "mvapich-discuss" <mvapich-discuss at cse.ohio-state.edu>
Betreff: [mvapich-discuss] mvapich and gromacs4.6
Datum: Sa., Nov 16, 2013 18:11


Dear Yang, 


To make sure I understand you correctly, you are seeing an issue when running Gromacs across two or more GPUs on the same node, using MVAPICH2? 


MVAPICH2 does has support for GPU-GPU MPI communication on multi-GPU nodes. Can you give some more information below about the issue? 


the configure options you used to build the library 


the command you are using for the run 


a backtrace, if its a hang, or the error, if its a failure



configuration of the nodes


This will help us see what could be going on. 


Best
Sreeram Potluri



On Fri, Nov 15, 2013 at 7:28 AM, <hpc at lzu.edu.cn> wrote:
Dear All

   I want to install gromacs4.6 at infiniband network.I installed the mvapich2-2.0a, gromacs4.6 support the GPUs,but when I running mpirun with mvapich,I found mvapich is only running one GPU, if I use two or more GPU, gromacs is not running. Anyone meet this problem? openmpi is support muliti-GPU.I don not know if the mvapich is only support one GPU. Maybe I install process have problem. anyone have suggestion for me, I am very appreciate. thanks!

Best wishes


yang

_______________________________________________
mvapich-discuss mailing list
mvapich-discuss at cse.ohio-state.edu
http://mailman.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss






-----------------------------------------------------------------------------------
Nvidia GmbH
Würselen
Amtsgericht Aachen
HRB 8361
Managing Director: Karen Theresa Burns

-----------------------------------------------------------------------------------
This email message is for the sole use of the intended recipient(s) and may contain
confidential information.  Any unauthorized review, use, disclosure or distribution
is prohibited.  If you are not the intended recipient, please contact the sender by
reply email and destroy all copies of the original message.
-----------------------------------------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.cse.ohio-state.edu/pipermail/mvapich-discuss/attachments/20131118/18e2e7cf/attachment-0001.html>