<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV id=yiv572359016>
<DIV>Hi all,</DIV>
<DIV> </DIV>
<DIV>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.</DIV>
<DIV> </DIV>
<DIV>Thanks,</DIV>
<DIV> </DIV>
<DIV>Juliana.<BR></DIV>
<DIV><BR>> I have installed in my pc centOS 5.2 with gcc 4.1.2 and i had some <BR>> problems when i had ran the gmxtest. The output is posted below:<BR>> ./gmxtest.pl all<BR>> *** glibc detected *** mdrun: realloc(): invalid next size: 0x09e070d0 ***<BR>> ======= Backtrace: =========<BR>> /lib/libc.so.6[0xb0d440]<BR>> /lib/libc.so.6(realloc+0x1a7)[0xb0e377]<BR>> mdrun[0x8136675]<BR>> ======= Memory map: ========<BR>> 00101000-00200000 r-xp 00000000 fd:00 250620 /usr/lib/libX11.so.6.2.0<BR>> 00200000-00204000 rwxp 000ff000 fd:00 250620 /usr/lib/libX11.so.6.2.0<BR>> 00204000-00205000 rwxp 00204000 00:00 0<BR>> 002bf000-002c0000 rwxp 002bf000 00:00 0<BR>> 004c7000-004c8000 rwxp 004c7000 00:00 0<BR>> 00835000-00848000 r-xp 00000000 fd:00 197077 /lib/libnsl-2.5.so<BR>> 00848000-00849000 r-xp 00012000 fd:00 197077
/lib/libnsl-2.5.so<BR>> 00849000-0084a000 rwxp 00013000 fd:00 197077 /lib/libnsl-2.5.so<BR>> 0084a000-0084c000 rwxp 0084a000 00:00 0<BR>> 008bb000-008bc000 r-xp 008bb000 00:00 0 [vdso]<BR>> 008bf000-008c0000 rwxp 008bf000 00:00 0<BR>> 009e8000-009f0000 r-xp 00000000 fd:00 250635 /usr/lib/libSM.so.6.0.0<BR>> 009f0000-009f1000 rwxp 00007000 fd:00 250635 /usr/lib/libSM.so.6.0.0<BR>> 009fa000-00a11000 r-xp 00000000 fd:00 250634 /usr/lib/libICE.so.6.3.0<BR>> 00a11000-00a12000 rwxp 00016000 fd:00 250634 /usr/lib/libICE.so.6.3.0<BR>> 00a12000-00a14000 rwxp 00a12000 00:00 0<BR>> 00a7f000-00a99000 r-xp 00000000 fd:00 197064 /lib/ld-2.5.so<BR>> 00a99000-00a9a000 r-xp 00019000 fd:00 197064 /lib/ld-2.5.so<BR>>
00a9a000-00a9b000 rwxp 0001a000 fd:00 197064 /lib/ld-2.5.so<BR>> 00a9d000-00a9f000 r-xp 00000000 fd:00 250618 /usr/lib/libXau.so.6.0.0<BR>> 00a9f000-00aa0000 rwxp 00001000 fd:00 250618 /usr/lib/libXau.so.6.0.0<BR>> 00aa2000-00bdf000 r-xp 00000000 fd:00 197065 /lib/libc-2.5.so<BR>> 00bdf000-00be1000 r-xp 0013c000 fd:00 197065 /lib/libc-2.5.so<BR>> 00be1000-00be2000 rwxp 0013e000 fd:00 197065 /lib/libc-2.5.so<BR>> 00be2000-00be5000 rwxp 00be2000 00:00 0<BR>> 00be7000-00c0c000 r-xp 00000000 fd:00 197072 /lib/libm-2.5.so<BR>> 00c0c000-00c0d000 r-xp 00024000 fd:00 197072 /lib/libm-2.5.so<BR>> 00c0d000-00c0e000 rwxp 00025000 fd:00 197072 /lib/libm-2.5.so<BR>> 00c10000-00c12000 r-xp 00000000 fd:00
197066 /lib/libdl-2.5.so<BR>> 00c12000-00c13000 r-xp 00001000 fd:00 197066 /lib/libdl-2.5.so<BR>> 00c13000-00c14000 rwxp 00002000 fd:00 197066 /lib/libdl-2.5.so<BR>> 00d30000-00d35000 r-xp 00000000 fd:00 250619 <BR>/usr/lib/libXdmcp.so.6.0.0<BR>> 00d35000-00d36000 rwxp 00004000 fd:00 250619 <BR>/usr/lib/libXdmcp.so.6.0.0<BR>> 049e1000-049ec000 r-xp 00000000 fd:00 197087 <BR>> /lib/libgcc_s-4.1.2-20080102.so.1<BR>> 049ec000-049ed000 rwxp 0000a000 fd:00 197087 <BR>> /lib/libgcc_s-4.1.2-20080102.so.1<BR>> 08048000-082f8000 r-xp 00000000 fd:00 1104196 <BR>> /usr/local/gromacs/bin/mdrun<BR>> 082f8000-082ff000 rwxp 002b0000 fd:00 1104196 <BR>> /usr/local/gromacs/bin/mdrun<BR>> 082ff000-08304000 rwxp 082ff000 00:00 0<BR>>
09df4000-09e15000 rwxp 09df4000 00:00 0<BR>> b7e00000-b7e21000 rwxp b7e00000 00:00 0<BR>> b7e21000-b7f00000 --xp b7e21000 00:00 0<BR>> bfdbd000-bfdd4000 rwxp bfdbd000 00:00 0 [stack]<BR>> sh: line 1: 17103 Abortado mdrun > mdrun.out 2>&1<BR>> FAILED. Check files in rb1<BR>> 1 out of 16 simple tests FAILED<BR>> FAILED. Check files in dec+water<BR>> 1 out of 14 complex tests FAILED<BR>> All 63 kernel tests PASSED<BR>> All 45 pdb2gmx tests PASSED<BR>> I have tried install the gromacs in another machine with Fedora Core 3 <BR>> and the gcc 3.4.4 and i have got similar result<BR>> ./gmxtest.pl all<BR>> *** glibc detected *** realloc(): invalid next size: 0x08a48f88 ***<BR>> sh: line 1: 12569
Aborted mdrun >mdrun.out 2>&1<BR>> FAILED. Check files in rb1<BR>> 1 out of 16 simple tests FAILED<BR>> FAILED. Check files in dec+water<BR>> 1 out of 14 complex tests FAILED<BR>> All 63 kernel tests PASSED<BR>> All 45 pdb2gmx tests PASSED<BR>> <BR>> So I think that the problem is not because i have used in the firts <BR>> machine the gcc 4.1.2 compiler. I have seen similar problems in the <BR>> mailing list, but i didn't find any solutions. Can anybody help me?<BR>> <BR>> Thanks,<BR>> <BR>> Juliana.<BR></DIV></DIV></td></tr></table><br>
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