AMBER Archive (2006)

Subject: RE: AMBER: Problem with shared libraries: libimf.so

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri May 05 2006 - 16:08:31 CDT

You need to apply the bugfixes to the source before you compile.

Go to: http://amber.scripps.edu/bugfixes80.html

Download bugfix.all. Then cd $AMBERHOME/src/

make clean
patch -p0 -N -r patch_rejects <bugfix.all
make
cd ../test
make clean
make

There were a number of bugs in the amber 8 QMMM implementation that can
cause segfaults on various machines. The bugfixes should fix the problem.

All the best
Ross

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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Priti Hansia
> Sent: Friday, May 05, 2006 11:40
> To: amber_at_scripps.edu
> Subject: RE: AMBER: Problem with shared libraries: libimf.so
>
>
> Dear Ross,
>
> I can't locate libimf.so on my system ! I have downloaded
> both ifort and
> mkl from intel website and installed them. But there seems to
> be no file
> called 'libimf.so' in the lib directory where the intel compiler is
> installed.
>
> However, adding ' source /opt/intel/fce/9.0/bin/ifortvars.sh
> ' to .bashrc
> worked :) I then started running 'make test' which seemed to
> be working
> until it gave the following error:
>
> cd qmmm/divcon; ./Run.crambin
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> sander.QMMM 080DCD3D Unknown Unknown Unknown
> sander.QMMM 080DB598 Unknown Unknown Unknown
> sander.QMMM 0808AD6F Unknown Unknown Unknown
> sander.QMMM 0806818A Unknown Unknown Unknown
> sander.QMMM 080649B2 Unknown Unknown Unknown
> sander.QMMM 0804A3E5 Unknown Unknown Unknown
> libc.so.6 B7C7C34E Unknown Unknown Unknown
> sander.QMMM 0804A321 Unknown Unknown Unknown
> ./Run.crambin: Program error
> make: *** [test.sander.QMMM] Error 1
>
> I also tried the static installation but there also I encountered some
> problem. I am attching the config.h file and the error message.
>
> -Priti
>
>
>
> > Dear Priti,
> >
> > Check where libimf.so is on your system:
> >
> > locate libimf.so
> >
> > This should be in the lib directory where the intel compiler is
> installed.
> > You can then either make sure this directory is in your
> path by manually
> adding it or make sure that you source the Intel setup script in your
> .bashrc or .cshrc as specified in the ifort manual. E.g.:
> >
> > source /opt/intel/fce/9.0/bin/ifortvars.sh
> >
> > If the problem still happens after this then it is likely to be some
> incompatibility between the operating system and the intel
> compilers. I
> would contact Intel support about the issue.
> >
> > Another option you could try is to compile AMBER statically:
> >
> > cd $AMBERHOME/src
> > ./configure -p4 -static ifort
> > make clean
> > make
> >
> > This should make the problem go away...
> >
> > All the best
> > Ross
>
>
>
>
>

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