AMBER Archive (2007)

Subject: Re: RE: Re: AMBER: on PATH

From: Alexandar T Tzanov (alex.tzanov_at_nyu.edu)
Date: Thu Jun 28 2007 - 10:39:57 CDT

Hi guys
I am installing Amber9 on Altix under Suse10 and I am getting from the test:

cd qmmm2/crambin_2; ./Run.crambin
*** glibc detected *** ../../../exe/sander: malloc(): memory corruption: 0x6000000000e75c90 ***
======= Backtrace: =========
/lib/libc.so.6.1[0x2000000000596f50]
/lib/libc.so.6.1[0x200000000059c4f0]
/lib/libc.so.6.1(malloc+0x559908)[0x20000000005a05e0]
../../../exe/sander[0x4000000000ed9f20]
../../../exe/sander[0x400000000006c740]
../../../exe/sander[0x40000000004492f0]
../../../exe/sander[0x40000000001936c0]
../../../exe/sander[0x400000000018de30]
../../../exe/sander[0x4000000000004700]
/lib/libc.so.6.1(__libc_start_main+0x4a7da8)[0x20000000004efc20]
../../../exe/sander[0x4000000000004480]
======= Memory map: ========
00000000-00004000 r--p 00000000 00:00 0
2000000000000000-2000000000038000 r-xp 00000000 08:03 25166467 /lib/ld-2.4.so
2000000000038000-200000000003c000 rw-p 2000000000038000 00:00 0
2000000000044000-200000000004c000 rw-p 00034000 08:03 25166467 /lib/ld-2.4.so
200000000004c000-20000000000cc000 r-xp 00000000 08:04 537398428 /usr/local/intel/cc/9.1.047/lib/libguide.so
20000000000cc000-20000000000d8000 ---p 00080000 08:04 537398428 /usr/local/intel/cc/9.1.047/lib/libguide.so
20000000000d8000-20000000000dc000 rw-p 0007c000 08:04 537398428 /usr/local/intel/cc/9.1.047/lib/libguide.so
20000000000dc000-20000000000e4000 rw-p 20000000000dc000 00:00 0
20000000000f8000-200000000011c000 r-xp 00000000 08:03 25191945 /lib/libpthread-2.4.so
200000000011c000-2000000000128000 ---p 00024000 08:03 25191945 /lib/libpthread-2.4.so
2000000000128000-2000000000130000 rw-p 00020000 08:03 25191945 /lib/libpthread-2.4.so
2000000000130000-2000000000134000 rw-p 2000000000130000 00:00 0
2000000000134000-200000000013c000 r-xp 00000000 08:03 25191925 /lib/libdl-2.4.so
200000000013c000-2000000000148000 ---p 00008000 08:03 25191925 /lib/libdl-2.4.so
2000000000148000-200000000014c000 rw-p 00004000 08:03 25191925 /lib/libdl-2.4.so
200000000014c000-20000000003b0000 r-xp 00000000 08:04 537398433 /usr/local/intel/cc/9.1.047/lib/libimf.so.6
20000000003b0000-20000000003bc000 ---p 00264000 08:04 537398433 /usr/local/intel/cc/9.1.047/lib/libimf.so.6
20000000003bc000-20000000003fc000 rw-p 00260000 08:04 537398433 /usr/local/intel/cc/9.1.047/lib/libimf.so.6
20000000003fc000-20000000004b8000 r-xp 00000000 08:03 25191927 /lib/libm-2.4.so
20000000004b8000-20000000004c4000 ---p 000bc000 08:03 25191927 /lib/libm-2.4.so
20000000004c4000-20000000004cc000 rw-p 000b8000 08:03 25191927 /lib/libm-2.4.so
20000000004cc000-2000000000704000 r-xp 00000000 08:03 25191919 /lib/libc-2.4.so
2000000000704000-2000000000710000 ---p 00238000 08:03 25191919 /lib/libc-2.4.so
2000000000710000-2000000000718000 rw-p 00234000 08:03 25191919 /lib/libc-2.4.so
2000000000718000-200000000071c000 rw-p 2000000000718000 00:00 0
200000000071c000-200000000072c000 r-xp 00000000 08:03 25750319 /lib/libgcc_s.so.1
200000000072c000-2000000000738000 ---p 00010000 08:03 25750319 /lib/libgcc_s.so.1
2000000000738000-200000000073c000 rw-p 0000c000 08:03 25750319 /lib/libgcc_s.so.1
200000000073c000-2000000000758000 r-xp 00000000 08:03 25225951 /lib/libunwind.so.7.0.0
2000000000758000-2000000000764000 ---p 0001c000 08:03 25225951 /lib/libunwind.so.7.0.0
2000000000764000-2000000000768000 rw-p 00018000 08:03 25225951 /lib/libunwind.so.7.0.0
2000000000768000-2000000000af4000 rw-p 2000000000768000 00:00 0
2000000000b00000-2000000000b24000 rw-p 2000000000b00000 00:00 0
2000000000b24000-2000000000c00000 ---p 2000000000b24000 00:00 0
4000000000000000-4000000000fd4000 r-xp 00000000 08:04 604483217 /usr/local/amber9/exe/sander
6000000000000000-60000000000bc000 rw-p 00fd0000 08:04 604483217 /usr/local/amber9/exe/sander
60000000000bc000-6000000000f10000 rw-p 60000000000bc000 00:00 0 [heap]
603fffffffffc000-6040000000000000 rw-p 603fffffffffc000 00:00 0
607ffffffe200000-607ffffffe254000 rwxp 607ffffffe200000 00:00 0 [stack]
a000000000000000-a000000000020000 ---p 00000000 00:00 0 [vdso]

Anybody to see such a thing before under Intel 9.1.047?

Thanks
Alex

----- Original Message -----
From: Ross Walker <ross_at_rosswalker.co.uk>
Date: Thursday, June 28, 2007 11:36 am
Subject: RE: Re: AMBER: $AMBERHOME on PATH
To: amber_at_scripps.edu

> Hi Francesco,
>
> > ./configure -static ifort_x86_64
> > ./configure: line 1264: config.h: Permission denied
>
> The issue is one of Unix file permissions. I suspect that you don't
> own the
> amber9 directory and all sub files. You have one of two options, either
> chown the directory to yourself and then repeat the installation or do
> the
> installation as root - which you tried...
>
> If you run the installation as root you have to make sure that root
> picks up
> all the environment variables etc. Thus it is probably easier to just
> chown
> everything to you.
>
> su -
> cd /path_to_amber9/
> cd ../
> chown -R username amber9 (where username is your username)
> exit (quits as root and should be back as your
> user)
>
> cd $AMBERHOME/src/
> ./configure -static ifort_x86_64
> make clean
> make
>
> If you get ifort not found then make sure you have modified your ~/.bashrc
> or ~/.cshrc (depending on your shell) to source
> /opt/intel/fce/9.1.036/bin/ifortvars.sh (or .csh if c shell)
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may
> not
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> issues.
>
>
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