[gmx-developers] problems in debugging process

[Mark Abraham]

Hi,

Debugging MPI programs is tricky - I strongly suggest that you start out
with the default non-MPI build of GROMACS (and even run that in
single-process mode with -ntmpi 1), so that you have fewer pieces of
infrastructure that you need to learn to manage correctly. Also, check
whether your local compute centers give access to TotalView or DDT
graphical MPI debuggers that will manage all these things for you.

Mark

On Thu, Mar 8, 2018 at 1:58 AM 1004753465 <1004753465 at qq.com> wrote:

> Hello everyone,
>
> I am trying to correct the velocity of atoms at every md step but I meet
> some problems so I would love to debug the mdrun of gromacs. but when I
> install the gromacs changed with DEBUG mode on and use xterm, it does no
> work.
>
> I follow the instructions on the website.My debug script is
>
> #!/bin/csh -f
> xterm -e gdb -x gdb_cmds ~/gromacs2018_debuginstall/usr/local/gromacs/bin/mdrun_mpi
>
> and my gdb_cmds is
>
> break reco_cal_vel
> run -v
>
> in which recp_cal_vel is a function I write and put in mdlib.
>
> but when I use
>
> mpirun -np 2 ./DEBUG
>
> to debug it, it just comes out
>
> [mpiexec at huan-Inspiron-5548] HYD_pmcd_pmi_alloc_pg_scratch (pm/pmiserv/pmiserv_utils.c:527): failed to allocate -24 bytes
> [mpiexec at huan-Inspiron-5548] HYD_pmci_launch_procs (pm/pmiserv/pmiserv_pmci.c:108): error allocating pg scratch space
> Segmentation fault (core dumped)
>
> I do not know what happens.Then I gave up the DEBUG script and tried
>
> mpirun -np 2 xterm -e gdb /home/huan/gromacs2018_debuginstall/usr/local/gromacs/bin/mdrun_mpi
>
> it came out 2 windows in xterm. I set two break points at the same function in both windows and then type "run" in both windows, then both of them disappeared.
>
> So how can I fix this problem? also, I wonder where I can put the .tpr files in the  debug process of mdrun_mpi?
>
> Thank you for your help!
>
> Regards,
>
> Helena
>
> Shanghai Jiao Tong University
>
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_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-developers
> or send a mail to gmx-developers-request at gromacs.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20180308/dd515774/attachment-0003.html>