[gmx-users] gmxtest rb1
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 15 10:10:19 CEST 2008
Juliana Angeiras wrote:
>
> Hi all,
>
> I'm still having problems with the simple test in the directory rb1. I
> have used gromacs 3.3.3 and gmxtest 3.3.3. The simple test in the
> directory simple/rb1/ crashed. The complex test dec+water too, but the
> problem seems not too serious as the related in the wiki. The
> configuration and the output are below.
>
Hi Juliana,
I have reproduced this bug. It has been fixed in the most recent CVS but
not in the 3.3.3 tree. A fix will be in release 4.0.1. I willhave a
quick look to see whether it is easy to port the fixes to 3.3 (although
we would like everyone to upgrade to 4.0).
> Thanks,
>
> Juliana.
>
> > I have installed in my pc centOS 5.2 with gcc 4.1.2 and i had some
> > problems when i had ran the gmxtest. The output is posted below:
> > ./gmxtest.pl all
> > *** glibc detected *** mdrun: realloc(): invalid next size:
> 0x09e070d0 ***
> > ======= Backtrace: =========
> > /lib/libc.so.6[0xb0d440]
> > /lib/libc.so.6(realloc+0x1a7)[0xb0e377]
> > mdrun[0x8136675]
> > ======= Memory map: ========
> > 00101000-00200000 r-xp 00000000 fd:00 250620 /usr/lib/libX11.so.6.2.0
> > 00200000-00204000 rwxp 000ff000 fd:00 250620 /usr/lib/libX11.so.6.2.0
> > 00204000-00205000 rwxp 00204000 00:00 0
> > 002bf000-002c0000 rwxp 002bf000 00:00 0
> > 004c7000-004c8000 rwxp 004c7000 00:00 0
> > 00835000-00848000 r-xp 00000000 fd:00 197077 /lib/libnsl-2.5.so
> > 00848000-00849000 r-xp 00012000 fd:00 197077 /lib/libnsl-2.5.so
> > 00849000-0084a000 rwxp 00013000 fd:00 197077 /lib/libnsl-2.5.so
> > 0084a000-0084c000 rwxp 0084a000 00:00 0
> > 008bb000-008bc000 r-xp 008bb000 00:00 0 [vdso]
> > 008bf000-008c0000 rwxp 008bf000 00:00 0
> > 009e8000-009f0000 r-xp 00000000 fd:00 250635 /usr/lib/libSM.so.6.0.0
> > 009f0000-009f1000 rwxp 00007000 fd:00 250635 /usr/lib/libSM.so.6.0.0
> > 009fa000-00a11000 r-xp 00000000 fd:00 250634 /usr/lib/libICE.so.6.3.0
> > 00a11000-00a12000 rwxp 00016000 fd:00 250634 /usr/lib/libICE.so.6.3.0
> > 00a12000-00a14000 rwxp 00a12000 00:00 0
> > 00a7f000-00a99000 r-xp 00000000 fd:00 197064 /lib/ld-2.5.so
> > 00a99000-00a9a000 r-xp 00019000 fd:00 197064 /lib/ld-2.5.so
> > 00a9a000-00a9b000 rwxp 0001a000 fd:00 197064 /lib/ld-2.5.so
> > 00a9d000-00a9f000 r-xp 00000000 fd:00 250618 /usr/lib/libXau.so.6.0.0
> > 00a9f000-00aa0000 rwxp 00001000 fd:00 250618 /usr/lib/libXau.so.6.0.0
> > 00aa2000-00bdf000 r-xp 00000000 fd:00 197065 /lib/libc-2.5.so
> > 00bdf000-00be1000 r-xp 0013c000 fd:00 197065 /lib/libc-2.5.so
> > 00be1000-00be2000 rwxp 0013e000 fd:00 197065 /lib/libc-2.5.so
> > 00be2000-00be5000 rwxp 00be2000 00:00 0
> > 00be7000-00c0c000 r-xp 00000000 fd:00 197072 /lib/libm-2.5.so
> > 00c0c000-00c0d000 r-xp 00024000 fd:00 197072 /lib/libm-2.5.so
> > 00c0d000-00c0e000 rwxp 00025000 fd:00 197072 /lib/libm-2.5.so
> > 00c10000-00c12000 r-xp 00000000 fd:00 197066 /lib/libdl-2.5.so
> > 00c12000-00c13000 r-xp 00001000 fd:00 197066 /lib/libdl-2.5.so
> > 00c13000-00c14000 rwxp 00002000 fd:00 197066 /lib/libdl-2.5.so
> > 00d30000-00d35000 r-xp 00000000 fd:00 250619
> /usr/lib/libXdmcp.so.6.0.0
> > 00d35000-00d36000 rwxp 00004000 fd:00 250619
> /usr/lib/libXdmcp.so.6.0.0
> > 049e1000-049ec000 r-xp 00000000 fd:00 197087
> > /lib/libgcc_s-4.1.2-20080102.so.1
> > 049ec000-049ed000 rwxp 0000a000 fd:00 197087
> > /lib/libgcc_s-4.1.2-20080102.so.1
> > 08048000-082f8000 r-xp 00000000 fd:00 1104196
> > /usr/local/gromacs/bin/mdrun
> > 082f8000-082ff000 rwxp 002b0000 fd:00 1104196
> > /usr/local/gromacs/bin/mdrun
> > 082ff000-08304000 rwxp 082ff000 00:00 0
> > 09df4000-09e15000 rwxp 09df4000 00:00 0
> > b7e00000-b7e21000 rwxp b7e00000 00:00 0
> > b7e21000-b7f00000 --xp b7e21000 00:00 0
> > bfdbd000-bfdd4000 rwxp bfdbd000 00:00 0 [stack]
> > sh: line 1: 17103 Abortado mdrun > mdrun.out 2>&1
> > FAILED. Check files in rb1
> > 1 out of 16 simple tests FAILED
> > FAILED. Check files in dec+water
> > 1 out of 14 complex tests FAILED
> > All 63 kernel tests PASSED
> > All 45 pdb2gmx tests PASSED
> > I have tried install the gromacs in another machine with Fedora Core 3
> > and the gcc 3.4.4 and i have got similar result
> > ./gmxtest.pl all
> > *** glibc detected *** realloc(): invalid next size: 0x08a48f88 ***
> > sh: line 1: 12569 Aborted mdrun >mdrun.out 2>&1
> > FAILED. Check files in rb1
> > 1 out of 16 simple tests FAILED
> > FAILED. Check files in dec+water
> > 1 out of 14 complex tests FAILED
> > All 63 kernel tests PASSED
> > All 45 pdb2gmx tests PASSED
> >
> > So I think that the problem is not because i have used in the firts
> > machine the gcc 4.1.2 compiler. I have seen similar problems in the
> > mailing list, but i didn't find any solutions. Can anybody help me?
> >
> > Thanks,
> >
> > Juliana.
>
>
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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