[AMBER-Developers] PMEMD and valgrind

From: Mark Williamson <mjw.sdsc.edu>
Date: Sat, 29 Aug 2009 01:59:50 +0100

Dear All,

I've just been passing a uni proc build of PMEMD through the memory
allocation checker tool Valgrind for unrelated reasons to the contents
of this email and I've found some issues. I think I've fixed these (make
test.pmemd is passing), but I just want to check If I have fixed them
correctly. Feedback would be great :)

PMEMD was built as follows from latest amber11 cvs co:

        ./configure linux_em64t gfortran nopar

generated config.h modded as follows:

        F90_OPT_DBG = -g
        ...
        F90_OPT_DFLT = $(F90_OPT_DBG)

Built using:
        make ; make install

Tested on the gb_mb benchmark:

        cd amber11/benchmarks/gb_mb
diff -r10.0 bench.gb_mb
28c28
< /bin/rm restrt gbin mdinfo 
---
 > #/bin/rm restrt gbin mdinfo
	./bench.gb_mb
	ln -s gbin mdin
Valgrind invoked as follows:
	valgrind --tool=memcheck -q ~/code/AMBER/amber11/exe/pmemd -O
Issue 1)
-=-=-=-=
| WARNING: Stack usage limited by a hard resource limit of  536870912 bytes!
|          If segment violations occur, get your sysadmin to increase the
limit.
==26884== Conditional jump or move depends on uninitialised value(s)
==26884==    at 0x464C83: __shake_mod__get_water_distances (shake.f90:647)
==26884==    by 0x465C9D: __shake_mod__shake_setup (shake.f90:369)
==26884==    by 0x47CDCE: MAIN__ (pmemd.f90:127)
==26884==    by 0x4A4BED: main (in
/server-home/mjw/code/AMBER/amber11/bin/pmemd)
==26884==
    atm_i = gbl_bond(j)%atm_i
     atm_j = gbl_bond(j)%atm_j
     parm_idx = gbl_bond(j)%parm_idx
     if (atm_i .eq. iof .and. atm_j .eq. ihf1) then      !<--shake.f90:647
       roh1 = gbl_req(parm_idx)
     else if (atm_j .eq. iof .and. atm_i .eq. ihf1) then
       roh1 = gbl_req(parm_idx)
     else if (atm_i .eq. iof .and. atm_j .eq. ihf2) then
I think this is fixed with:
[16:59][bunny:0.12][mjw:src]$ cvs diff shake.fpp
Index: shake.fpp
===================================================================
RCS file: /home/amber_cvs/cvsroot/amber11/src/pmemd/src/shake.fpp,v
retrieving revision 10.1
diff -r10.1 shake.fpp
834a835,838
 >   iof = 0
 >   ihf1 = 0
 >   ihf2 = 0
 >
840,842d843
<     iof = 0
<     ihf1 = 0
<     ihf2 = 0
Issue 2
-=-=-=-=
==15652== Invalid write of size 4
==15652==    at 0x46E52A: __gb_ene_mod__gb_ene (gb_ene.f90:630)
==15652==    by 0x472BED: __gb_force_mod__gb_force (gb_force.f90:143)
==15652==    by 0x45E658: __runmd_mod__runmd (runmd.f90:344)
==15652==    by 0x47D188: MAIN__ (pmemd.f90:194)
==15652==    by 0x4A4C5D: main (in
/server-home/mjw/code/AMBER/amber11/bin/pmemd)
     do jjv = jexcl, jexcl_last
       skipv(natex(jjv)) = .true.   <---------gb_ene.f90:630
     end do
This is happening because some values of natex() are actually zero, 
hence skipv(0) is being set to .true. This patch fixes it:
Index: gb_ene.fpp
===================================================================
RCS file: /home/amber_cvs/cvsroot/amber11/src/pmemd/src/gb_ene.fpp,v
retrieving revision 10.1
diff -r10.1 gb_ene.fpp
612c612,614
<       skipv(natex(jjv)) = .true.
---
 >       if (natex(jjv) .ne. 0 ) then !natex(jjv) can contain zero values
 >        skipv(natex(jjv)) = .true.
 >       end if
regards,
Mark
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Received on Wed Sep 02 2009 - 23:06:04 PDT
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