Dear Dac,
For making the installation more smooth, we decided to install from scratch. We plan to install openmpi-1.4.4 and amber9. Unfortunately in the first step it self we encounter some error. Here I would like to post our steps in order to get some help from experts from this community.
The steps:
1) Installation Intel-MKL library. - done by SGI engineers
2) Installation openmpi-1.4.4
2.1) We place the openmpi-1.4.4 folder at /mnt/data1/application/
2.2) Next we execute configure command with this options
../configure -enable-debug -enable-mem-debug --prefix=/mnt/data1/application/openmpi-1.4.4 CC=/mnt/data/cluster/intel/cce/10.1.008/bin/icc FC=/mnt/data/cluster/intel/fce/10.1.008/bin/ifort CXX=/mnt/data/cluster/intel/cce/10.1.008/bin/icpc
2.3) After this, we execute make command.,and we get errors as below:
/usr/include/mpi.h(179): error: expected an identifier
MPI_ERR_FILE_EXISTS = 36,
^
/usr/include/mpi.h(180): error: expected an identifier
MPI_ERR_FILE_IN_USE = 37,
^
/usr/include/mpi.h(181): error: expected an identifier
MPI_ERR_FILE = 38,
^
compilation aborted for ../../../../../../../../ompi/mca/io/romio/romio/adio/common/ad_aggregate.c (code 4)
make[5]: *** [ad_aggregate.lo] Error 1
make[5]: Leaving directory `/mnt/data1/application/openmpi-1.4.4/build/ompi/mca/io/romio/romio/adio/common'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/mnt/data1/application/openmpi-1.4.4/build/ompi/mca/io/romio/romio/adio'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/mnt/data1/application/openmpi-1.4.4/build/ompi/mca/io/romio/romio'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/mnt/data1/application/openmpi-1.4.4/build/ompi/mca/io/romio'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/data1/application/openmpi-1.4.4/build/ompi'
make: *** [all-recursive] Error 1
ptmlxclus:/mnt/data1/application/openmpi-1.4.4/build #
We are lost at this level itself. Is there any way to fix this issue. Any help appreciated in advance.
Regards
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
________________________________
From: David A Case <case.biomaps.rutgers.edu>
To: Vijay Manickam Achari <vjrajamany.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, 15 November 2011, 20:53
Subject: Re: [AMBER] Installing AMBER9 in SGI_ALTIX-XE1300 - need some help
On Tue, Nov 15, 2011, Vijay Manickam Achari wrote:
>
> I am compiling AMBER9 in
> SGI_ALTIXÂ XE1300. The command I used was as below. But it shows
> error. I have cut and paste the output that I got. Sorry it is quite
> long.
Try undefining MKL_HOME.
I'm printing below the key messages...maybe someone who still has ALTIX
machines (or who has a good memory) will recognize something. Another thing
to try is to leave out the -static flag when you run configure.
....dac
> ld: skipping incompatible /mnt/data/cluster/intel/mkl/10.0.010/lib/64/libmkl_intel_lp64.a when searching for libmkl_intel_lp64.a
> ld:
> skipping incompatible
> /mnt/data/cluster/intel/mkl/10.0.010/lib/64/libmkl_intel_thread.a when
> searching for libmkl_intel_thread.a
> ld: skipping incompatible /mnt/data/cluster/intel/mkl/10.0.010/lib/64/libmkl_core.a when searching for libmkl_core.a
> /mnt/data/cluster/intel/mkl/10.0.010/lib/em64t/libmkl_intel_thread.a(vml_threading_templates.o): In function
> `mkl_vml_service_threader_z_1i_c_1o':
> _tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x5a): undefined reference to `__kmpc_global_thread_num'
> _tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x131): undefined reference to `__kmpc_ok_to_fork'
> _tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x156): undefined reference to `__kmpc_push_num_threads'
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 16 2011 - 00:30:03 PST
