AMBER Archive (2006)

Subject: Re: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test

From: Roberto Gomperts (roberto_at_sgi.com)
Date: Wed Jun 21 2006 - 09:10:44 CDT

Hi David,

This problem (not altix specific) has been solved with bugfix #2. Please
make sure you patch your source (preferably) with bugfix.all to resolve
the latest known problems.
Please let me know if there are any issues after you apply the patch.

Thanks,
Roberto

David McGiven wrote:
> Dear Amber users,
>
> We recently bought amber 9 and I compiled it in one of our SGI machines.
>
> The Machine is an SGI Prism (Basically an Altix with Graphics) running
> SLES9 with SGI ProPack 4SP3 for Linux, Build 403r1-0512182217
>
> I compiled the amber9 source tarball with Intel 8.0 compilers :
>
> Those are the versions I used :
>
> l_cc_pc_8.1.032.tar.gz
> l_fc_pc_8.1.028.tar.gz
>
> I ran ./configure -nopar sgi_altix
> make serial
>
> The compilation was ok and then I started to run the tests. Everything
> was going fine till it reached the pbpgb test. It crashes with the
> following error :
>
> ==============================================================
> cd alp; ./Run.alp
> diffing mdout.alp.save with mdout.alp
> PASSED
> ==============================================================
> cd pb_pgb; ./Run.pbpgb
> getRegFromUnwindContext: Can't get Gr0 from UnwindContext, using 0
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line
> Source sander 40000000000AC821 Unknown
> Unknown Unknown sander 4000000000095300 Unknown
> Unknown Unknown sander 400000000008FA30 Unknown
> Unknown Unknown sander 40000000005EEBA0 Unknown
> Unknown Unknown sander 40000000001CB390 Unknown
> Unknown Unknown sander 4000000000177EF0
> Unknown Unknown Unknown sander
> 4000000000176730 Unknown Unknown Unknown sander
> 4000000000003E90 Unknown Unknown Unknown libc.so.6.1
> 2000000001AB9C50 Unknown Unknown Unknown sander
> 4000000000003840 Unknown Unknown Unknown
> ./Run.pbpgb: Program error make: *** [test.sander.BASIC] Error 1
>
>
> At the same time, in another folder, I was compiling it with mpi support
>
> I ran ./configure -mpi sgi_altix
> make parallel
>
> Again, the compilation was ok and then I started to run the tests.
> Everything was going fine till it reached the pbpgb test again!. It
> crashes with the following error :
>
> ==============================================================
> cd alp; ./Run.alp
> diffing mdout.alp.save with mdout.alp
> PASSED
> ==============================================================
> cd pb_pgb; ./Run.pbpgb
> MPI: On host incal, Program /opt/soft/amber9-mpi-mkl/exe/sander.MPI,
> Rank 0, Process 16286 received signal SIGSEGV(11)
>
>
> MPI: --------stack traceback-------
> sh: line 1: idb: command not found
>
> MPI: -----stack traceback ends-----
> MPI: On host incal, Program /opt/soft/amber9-mpi-mkl/exe/sander.MPI,
> Rank 0, Process 16286: Dumping core on signal SIGSEGV(11) into directory
> /opt/soft/amber9-mpi-mkl/test/pb_pgb MPI: MPI_COMM_WORLD rank 0 has
> terminated without calling MPI_Finalize() MPI: aborting job
> MPI: Received signal 11
>
> ./Run.pbpgb: Program error
> make[1]: *** [test.sander.BASIC] Error 1
> make[1]: Leaving directory `/opt/soft/amber9-mpi-mkl/test'
> make: *** [test.sander.BASIC.MPI] Error 2
>
>
> Best Regards,
> David McGiven
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> 

-- 
	Roberto Gomperts		VNET:   483-8851
	One Cabot Road, Suite 290	Phone: (978) 562-8851
	Hudson, MA 01749		Fax:   (978) 562-7450

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