[gmx-developers] problems in debugging process

1004753465 1004753465 at qq.com
Thu Mar 8 01:58:37 CET 2018

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!



Shanghai Jiao Tong University
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