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Bug #141

g_rdf hangs depending on the gcc compiler

Added by andrea spitaleri over 12 years ago. Updated over 12 years ago.

Status:
Closed
Priority:
High
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Hi all,
I have suspicious that g_rdf is bugged or at least it has a problem depending on
the machine type.
In one pc works and in another it hangs in "Reading frame 0.0000 0.0000". I
should also to say that
in the "PC not working" it hangs depending on the kind of selection done,
whereas in the other one
it always works fine and properly. In both machine gromacs has been compiled
with classic
./configure && make .
Version 3.3.1

PC working:
gcc version 4.0.2 20050901 (prerelease) (SUSE Linux)
Suse 10.0 2.6.13-15-smp

PC not working:
gcc version 4.1.2 20061115 (prerelease) (SUSE Linux)
Suse 10.2 2.6.18.2-34-default

avb3-rgd-300NPT.tpr (29.2 MB) avb3-rgd-300NPT.tpr tpr file andrea spitaleri, 04/11/2007 09:53 AM
index-8.ndx (5.29 MB) index-8.ndx index file andrea spitaleri, 04/11/2007 09:56 AM
avb3-rgd-1nsFin-Last500skip10.xtc (42 MB) avb3-rgd-1nsFin-Last500skip10.xtc trr file andrea spitaleri, 04/11/2007 10:26 AM
rdf.xvg (65 KB) rdf.xvg Resulting RDF David van der Spoel, 04/11/2007 10:40 AM

History

#1 Updated by Bruce D. over 12 years ago

(In reply to comment #0)

Hi all,
I have suspicious that g_rdf is bugged or at least it has a problem depending on
the machine type.
In one pc works and in another it hangs in "Reading frame 0.0000 0.0000". I
should also to say that
in the "PC not working" it hangs depending on the kind of selection done,
whereas in the other one
it always works fine and properly. In both machine gromacs has been compiled
with classic
./configure && make .
Version 3.3.1

PC working:
gcc version 4.0.2 20050901 (prerelease) (SUSE Linux)
Suse 10.0 2.6.13-15-smp

PC not working:
gcc version 4.1.2 20061115 (prerelease) (SUSE Linux)
Suse 10.2 2.6.18.2-34-default

Just a note on this from another user. I looked through the code for do_rdf
in gmx_rdf.c for Gromacs 3.3.1 and found the following apparent allocations
and freeings of memory:

Allocated Freed
______________________________
grpname
isize
index
index_cm
count
pairs
npairs
nself
bExcl bExcl
count[g]
pairs[g]
npairs[g]
pairs[g][i] pairs[g][i]
x_i1
inv_segvol
rdf rdf
rdf[g] rdf[g]
hq hq
integrand integrand
sum sum
x

It appears as if a number of memory allocations are made but nnot freed by
the time do_rdf exits. It also appears as if an attempt is made to free
some memory for which I cannot find an allocation. Perhaps these could be
contributing to the problem?

#2 Updated by David van der Spoel over 12 years ago

This is most likely a compiler problem. I'll be trying to set up a linux box
with similar specs to test it. Other tools seem to have the same problem when
compiled with gcc 4.1.x.

Please provide sample input that crashes.

#3 Updated by David van der Spoel over 12 years ago

Very likely this problem has been fixed due to a fix in bug 108. See:
http://bugzilla.gromacs.org/show_bug.cgi?id=108

If you can provide input that proves otherwise with the CVS 3.3 code you can
reopen the bug.

#4 Updated by andrea spitaleri over 12 years ago

Created an attachment (id=110)
tpr file

#5 Updated by andrea spitaleri over 12 years ago

Created an attachment (id=111)
index file

#6 Updated by David van der Spoel over 12 years ago

Now we need a short trajectory and a command line, including the selection of
the index groups.

#7 Updated by andrea spitaleri over 12 years ago

Created an attachment (id=112)
trr file

g_rdf -s avb3-rgd-300NPT.tpr -f avb3-rgd-1nsFin-Last500skip10.xtc -o tempo -n
index-8.ndx
select 12 and 18 group
rdf hangs in 0 1500
thanks

#8 Updated by David van der Spoel over 12 years ago

Created an attachment (id=113)
Resulting RDF

This works now as well. That probably means the workaround for the compiler bug
applies to this problem as well. The code is in CVS now. Please try the CVS
version with the release-3-3-patches.

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