[gmx-developers] valgrind

Roland Schulz roland at utk.edu
Fri Jul 2 10:06:10 CEST 2010

Hi Berk,

while I run valgrind I had a couple of errors (suppressing anything MPI

Thus I have a couple of questions:

What is our policy regarding uninitialized variables. Is it OK to leave
them uninitialized if they are not used or should they always be initialized
when they are indirectly used.
set_ddbox_cr doesn't set the members v or normal of ddbox (type gmx_ddbox_t)
and then bcast. valgrind of course sees this as an error because the bcast
reads the initialized variable.

If they should always be initialized, is it a good idea to initialize
static structs with "= {0}"? E.g. ddbox is declared in mdrunner as
      gmx_ddbox_t ddbox;
Should this be changed to:
      gmx_ddbox_t ddbox={0};

Or is there some reason not to use the "{0}" method to initialize? If the
{0} is OK than just let me know and I'll commit it. I have fixed it in 2

Do you have a valgrind suppression list with known false-positives?

Some of the errors I've seen:

==2841== Invalid read of size 4
==2841==    at 0x538CE1: gmx_pme_send_q_x (pme_pp.c:202)
==2841==    by 0x538E60: gmx_pme_send_q (pme_pp.c:237)
==2841==    by 0x462273: dd_partition_system (domdec.c:8550)
==2841==    by 0x4308EA: do_md (md.c:1259)
==2841==    by 0x42C6F2: mdrunner (runner.c:771)
==2841==    by 0x4377CC: main (mdrun.c:631)
==2841==  Address 0x7feffc4cc is on thread 1's stack

==2846== Uninitialised byte(s) found during client check request
==2846==    at 0x625C09D: valgrind_module_isdefined (in
==2846==    by 0x5D8547A: PMPI_Isend (in
==2846==    by 0x539B50: gmx_pme_send_force_vir_ener (pme_pp.c:507)
==2846==    by 0x536F8F: gmx_pmeonly (pme.c:2423)
==2846==    by 0x42C75E: mdrunner (runner.c:792)
==2846==    by 0x4377CC: main (mdrun.c:631)
==2846==  Address 0x7feffceb0 is on thread 1's stack

==2846== Conditional jump or move depends on uninitialised value(s)
==2846==    at 0x42C7F7: mdrunner (runner.c:800)
==2846==    by 0x4377CC: main (mdrun.c:631)
==2846== Conditional jump or move depends on uninitialised value(s)
==2846==    at 0x6B22760: __tzfile_compute (in /lib64/libc-2.5.so)
==2846==    by 0x6B221BE: __tz_convert (in /lib64/libc-2.5.so)
==2846==    by 0x6B20798: ctime (in /lib64/libc-2.5.so)
==2846==    by 0x54B9B1: print_date_and_time (sim_util.c:253)
==2846==    by 0x42C920: mdrunner (runner.c:821)
==2846==    by 0x4377CC: main (mdrun.c:631)


ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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