Dear Ambers,
I have recently compiled AMBER 11 + AT 1.5 on my new openSUSE 12.1 OS on
a x86_64 linux machine. Everything went smoothly and tests were successful.
However, I have a new problem when running xleap. I get the error below
while executing the $AMBERHOME/bin/xleap exec.
the glibc version is 2.14.1. The compiler is gnu 4.6.2.
I have seen similar errors in the archive but mostly related to ptraj
and not xleap
If anybody had seen this, i would appreciate any advice on how to get
rid of the problem
Thank you
Vlad
I: Adding /usr/local/apps/amber/11-1.5/dat/leap/prep to search path.
-I: Adding /usr/local/apps/amber/11-1.5/dat/leap/lib to search path.
-I: Adding /usr/local/apps/amber/11-1.5/dat/leap/parm to search path.
-I: Adding /usr/local/apps/amber/11-1.5/dat/leap/cmd to search path.
*** glibc detected *** /usr/local/apps/amber/11-1.5/bin/xaLeap: free():
invalid pointer: 0x00007f90b265d010 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x74c06)[0x7f90b0d8bc06]
/usr/lib64/libX11.so.6(+0x2f312)[0x7f90b1953312]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4fb9bb]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x496f88]
/usr/lib64/libXt.so.6(+0x16a1f)[0x7f90b22b3a1f]
/usr/lib64/libXt.so.6(_XtConvert+0xe6)[0x7f90b22b49c6]
/usr/lib64/libXt.so.6(+0x33b96)[0x7f90b22d0b96]
/usr/lib64/libXt.so.6(_XtGetResources+0x107)[0x7f90b22d1ae7]
/usr/lib64/libXt.so.6(+0x1d646)[0x7f90b22ba646]
/usr/lib64/libXt.so.6(_XtCreateWidget+0xeb)[0x7f90b22bab0b]
/usr/lib64/libXt.so.6(XtCreateWidget+0xde)[0x7f90b22bae1e]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ede51]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee4c2]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee0dd]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee471]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee4e8]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee0dd]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee471]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee4e8]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee0dd]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee471]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee4e8]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4edf54]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee426]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee735]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x497670]
/lib64/libc.so.6(__libc_start_main+0xed)[0x7f90b0d3823d]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x407789]
======= Memory map: ========
00400000-00548000 r-xp 00000000 08:19 3557037
/usr/local/apps/amber/11-1.5/bin/xaLeap
00747000-00748000 r--p 00147000 08:19 3557037
/usr/local/apps/amber/11-1.5/bin/xaLeap
00748000-0076f000 rw-p 00148000 08:19 3557037
/usr/local/apps/amber/11-1.5/bin/xaLeap
0076f000-0088e000 rw-p 00000000 00:00 0
[heap]
7f90afebe000-7f90afed3000 r-xp 00000000 08:16 1050997
/lib64/libgcc_s.so.1
7f90afed3000-7f90b00d2000 ---p 00015000 08:16 1050997
/lib64/libgcc_s.so.1
7f90b00d2000-7f90b00d3000 r--p 00014000 08:16 1050997
/lib64/libgcc_s.so.1
7f90b00d3000-7f90b00d4000 rw-p 00015000 08:16 1050997
/lib64/libgcc_s.so.1
7f90b00d4000-7f90b00d9000 r-xp 00000000 08:16 1050497
/usr/lib64/libXfixes.so.3.1.0
7f90b00d9000-7f90b02d9000 ---p 00005000 08:16 1050497
/usr/lib64/libXfixes.so.3.1.0
7f90b02d9000-7f90b02da000 r--p 00005000 08:16 1050497
/usr/lib64/libXfixes.so.3.1.0
7f90b02da000-7f90b02db000 rw-p 00006000 08:16 1050497
/usr/lib64/libXfixes.so.3.1.0
7f90b02db000-7f90b02e5000 r-xp 00000000 08:16 1050522
/usr/lib64/libXrender.so.1.3.0
7f90b02e5000-7f90b04e4000 ---p 0000a000 08:16 1050522
/usr/lib64/libXrender.so.1.3.0
7f90b04e4000-7f90b04e5000 r--p 00009000 08:16 1050522
/usr/lib64/libXrender.so.1.3.0
7f90b04e5000-7f90b04e6000 rw-p 0000a000 08:16 1050522
/usr/lib64/libXrender.so.1.3.0
7f90b04e6000-7f90b04ef000 r-xp 00000000 08:16 1050500
/usr/lib64/libXcursor.so.1.0.2
7f90b04ef000-7f90b06ef000 ---p 00009000 08:16 1050500
/usr/lib64/libXcursor.so.1.0.2
7f90b06ef000-7f90b06f0000 r--p 00009000 08:16 1050500
/usr/lib64/libXcursor.so.1.0.2
7f90b06f0000-7f90b06f1000 rw-p 0000a000 08:16 1050500
/usr/lib64/libXcursor.so.1.0.2
7f90b06f1000-7f90b06f3000 r-xp 00000000 08:16 1050878
/lib64/libdl-2.14.1.so
7f90b06f3000-7f90b08f3000 ---p 00002000 08:16 1050878
/lib64/libdl-2.14.1.so
7f90b08f3000-7f90b08f4000 r--p 00002000 08:16 1050878
/lib64/libdl-2.14.1.so
7f90b08f4000-7f90b08f5000 rw-p 00003000 08:16 1050878
/lib64/libdl-2.14.1.so
7f90b08f5000-7f90b0911000 r-xp 00000000 08:16 1057792
/usr/lib64/libxcb.so.1.1.0
7f90b0911000-7f90b0b10000 ---p 0001c000 08:16 1057792
/usr/lib64/libxcb.so.1.1.0
7f90b0b10000-7f90b0b11000 r--p 0001b000 08:16 1057792
/usr/lib64/libxcb.so.1.1.0
7f90b0b11000-7f90b0b12000 rw-p 0001c000 08:16 1057792
/usr/lib64/libxcb.so.1.1.0
7f90b0b12000-7f90b0b16000 r-xp 00000000 08:16 1050884
/lib64/libuuid.so.1.3.0
7f90b0b16000-7f90b0d15000 ---p 00004000 08:16 1050884
/lib64/libuuid.so.1.3.0
7f90b0d15000-7f90b0d16000 r--p 00003000 08:16 1050884
/lib64/libuuid.so.1.3.0
7f90b0d16000-7f90b0d17000 rw-p 00004000 08:16 1050884
/lib64/libuuid.so.1.3.0
7f90b0d17000-7f90b0e9c000 r-xp 00000000 08:16 1050999
/lib64/libc-2.14.1.so
7f90b0e9c000-7f90b109c000 ---p 00185000 08:16 1050999
/lib64/libc-2.14.1.so
7f90b109c000-7f90b10a0000 r--p 00185000 08:16 1050999
/lib64/libc-2.14.1.so
7f90b10a0000-7f90b10a1000 rw-p 00189000 08:16 1050999
/lib64/libc-2.14.1.so
7f90b10a1000-7f90b10a6000 rw-p 00000000 00:00 0
7f90b10a6000-7f90b10be000 r-xp 00000000 08:16 1050875
/lib64/libpthread-2.14.1.so
7f90b10be000-7f90b12bd000 ---p 00018000 08:16 1050875
/lib64/libpthread-2.14.1.so
7f90b12bd000-7f90b12be000 r--p 00017000 08:16 1050875
/lib64/libpthread-2.14.1.so
7f90b12be000-7f90b12bf000 rw-p 00018000 08:16 1050875
/lib64/libpthread-2.14.1.so
7f90b12bf000-7f90b12c3000 rw-p 00000000 00:00 0
7f90b12c3000-7f90b1319000 r-xp 00000000 08:16 1050847
/lib64/libm-2.14.1.so
7f90b1319000-7f90b1518000 ---p 00056000 08:16 1050847
/lib64/libm-2.14.1.so
7f90b1518000-7f90b1519000 r--p 00055000 08:16 1050847
/lib64/libm-2.14.1.so
7f90b1519000-7f90b151a000 rw-p 00056000 08:16 1050847
/lib64/libm-2.14.1.so
7f90b151a000-7f90b151f000 r-xp 00000000 08:16 1050516
/usr/lib64/libXdmcp.so.6.0.0
7f90b151f000-7f90b171e000 ---p 00005000 08:16 1050516
/usr/lib64/libXdmcp.so.6.0.0
7f90b171e000-7f90b171f000 r--p 00004000 08:16 1050516
/usr/lib64/libXdmcp.so.6.0.0
7f90b171f000-7f90b1720000 rw-p 00005000 08:16 1050516
/usr/lib64/libXdmcp.so.6.0.0
7f90b1720000-7f90b1722000 r-xp 00000000 08:16 1055609
/usr/lib64/libXau.so.6.0.0
7f90b1722000-7f90b1922000 ---p 00002000 08:16 1055609
/usr/lib64/libXau.so.6.0.0
7f90b1922000-7f90b1923000 r--p 00002000 08:16 1055609
/usr/lib64/libXau.so.6.0.0
7f90b1923000-7f90b1924000 rw-p 00003000 08:16 1055609
/usr/lib64/libXau.so.6.0.0
7f90b1924000-7f90b1a5f000 r-xp 00000000 08:16 1057798
/usr/lib64/libX11.so.6.3.0
7f90b1a5f000-7f90b1c5f000 ---p 0013b000 08:16 1057798
/usr/lib64/libX11.so.6.3.0
7f90b1c5f000-7f90b1c60000 r--p 0013b000 08:16 1057798
/usr/lib64/libX11.so.6.3.0
7f90b1c60000-7f90b1c65000 rw-p 0013c000 08:16 1057798
/usr/lib64/libX11.so.6.3.0
7f90b1c65000-7f90b1c7c000 r-xp 00000000 08:16 1055633
/usr/lib64/libICE.so.6.3.0
7f90b1c7c000-7f90b1e7b000 ---p 00017000 08:16 1055633
/usr/lib64/libICE.so.6.3.0
7f90b1e7b000-7f90b1e7c000 r--p 00016000 08:16 1055633
/usr/lib64/libICE.so.6.3.0
7f90b1e7c000-7f90b1e7d000 rw-p 00017000 08:16 1055633
/usr/lib64/libICE.so.6.3.0
7f90b1e7d000-7f90b1e81000 rw-p 00000000 00:00 0
7f90b1e81000-7f90b1e88000 r-xp 00000000 08:16 1055644
/usr/lib64/libSM.so.6.0.1
7f90b1e88000-7f90b2088000 ---p 00007000 08:16 1055644
/usr/lib64/libSM.so.6.0.1
7f90b2088000-7f90b2089000 r--p 00007000 08:16 1055644
/usr/lib64/libSM.so.6.0.1
7f90b2089000-7f90b208a000 rw-p 00008000 08:16 1055644
/usr/lib64/libSM.so.6.0.1
7f90b208a000-7f90b209b000 r-xp 00000000 08:16 1057894
/usr/lib64/libXext.so.6.4.0
7f90b209b000-7f90b229b000 ---p 00011000 08:16 1057894
/usr/lib64/libXext.so.6.4.0
7f90b229b000-7f90b229c000 r--p 00011000 08:16 1057894
/usr/lib64/libXext.so.6.4.0
7f90b229c000-7f90b229d000 rw-p 00012000 08:16 1057894
/usr/lib64/libXext.so.6.4.0
7f90b229d000-7f90b22fd000 r-xp 00000000 08:16 1055618
/usr/lib64/libXt.so.6.0.0
7f90b22fd000-7f90b24fd000 ---p 00060000 08:16 1055618
/usr/lib64/libXt.so.6.0.0
7f90b24fd000-7f90b24fe000 r--p 00060000 08:16 1055618
/usr/lib64/libXt.so.6.0.0
7f90b24fe000-7f90b2503000 rw-p 00061000 08:16 1055618
/usr/lib64/libXt.so.6.0.0
7f90b2503000-7f90b2504000 rw-p 00000000 00:00 0
7f90b2504000-7f90b2524000 r-xp 00000000 08:16 1050870
/lib64/ld-2.14.1.so
7f90b265d000-7f90b26a5000 rw-p 00000000 00:00 0
7f90b26ed000-7f90b26f5000 rw-p 00000000 00:00 0
7f90b2721000-7f90b2724000 rw-p 00000000 00:00 0
7f90b2724000-7f90b2725000 r--p 00020000 08:16 1050870
/lib64/ld-2.14.1.so
7f90b2725000-7f90b2726000 rw-p 00021000 08:16 1050870
/lib64/ld-2.14.1.so
7f90b2726000-7f90b2727000 rw-p 00000000 00:00 0
7ffff39b1000-7ffff39eb000 rw-p 00000000 00:00 0
[stack]
7ffff39ff000-7ffff3a00000 r-xp 00000000 00:00 0
[vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
[vsyscall]
/usr/local/apps/amber/11-1.5/bin/xleap: line 19: 17835
Aborted $AMBERHOME/bin/xaLeap -I$AMBERHOME/dat/leap/prep
-I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm
-I$AMBERHOME/dat/leap/cmd $*
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Mon Nov 28 2011 - 05:00:03 PST
