[molpro-user] Parallel Molpro 2002.6 on ALTIX 350
Jacek Klos
jakl at tiger.chem.uw.edu.pl
Thu Sep 15 15:11:54 BST 2005
Hi Nick,
It seems I have the MPT library installed:
sgi-mpt-1.10.1-sgi305r1
This RPM gives following libraries:
/usr/bin/mpirun
/usr/include/MPI.mod
/usr/include/MPI_INTERFACE.mod
/usr/include/mpi++.h
/usr/include/mpi.h
/usr/include/mpi.mod
/usr/include/mpi_ext.h
/usr/include/mpi_extf.h
/usr/include/mpif.h
/usr/include/mpif_parameters.h
/usr/include/mpio.h
/usr/include/mpiof.h
/usr/include/mpp
/usr/include/mpp/shmem.fh
/usr/include/mpp/shmem.h
/usr/lib/libmpi++.so
/usr/lib/libmpi.so
/usr/lib/libsma.so
/usr/lib/libxmpi.so
/usr/local/bin/mpi_launch
With USE_MPI=yes GA compiles and molpro 2002.6 links correctly, but
there are many test job failures (GA ERROR in the output).
I will try compiling molpro completely with -O1 level, this should give
less testjob failures I believe at the cost of performance.
As Ross suggested I will try to comment fastbcopy lines and try to compile
molpro with TCGMSG
Thank you all for help
Jacek
---------------------
Hi Jacek,
It looks as if fastbcopy comes with the sgi MPT library
http://www.sgi.com/products/evaluation/2.1_mpt_1.9_linux/page2.html
which looks as if it needs the SGI ProPack
http://oss.sgi.com/projects/sgi_propack/
Without the MPT library you you not be able access the shared memory NUMA
capabilities of an Altix. molpro also uses the dplace comand from the
numatools package to place the molpro executables on specific processors
which improves shared memory usage.
Best wishes,
Nick Wilson
Ross Nobes wrote:
Hi Jacek,
I am using the same compilers as you on Itanium hardware, but not on an
SGI Altix system. There is some special code in armci/src/copy.h for
Altix systems only, and hence I do not run into this fastbcopy problem.
If you really do not have access to fastbcopy, then you could disable
the following lines in armci/src/copy.h and then build the TCGMSG
version as I suggested earlier:
#if defined(LINUX64) && defined(SGIALTIX)
/* fastbcopy from Wayne Vieira and Gerardo Cisneros */
#define MEMCPY
#define armci_copy(src, dst, len) _fastbcopy(src, dst, len)
#define memcpy(dst, src, len) _fastbcopy(src, dst, len)
#define bcopy(src, dst, len) _fastbcopy(src, dst, len)
#endif
e.g. delete the lines above and then do
make TARGET=LINUX64 CC=icc FC=ifort
Cheers,
Ross
-----Original Message-----
From: Jacek Klos [mailto:jakl at tiger.chem.uw.edu.pl]
Sent: 14 September 2005 17:59
To: molpro-user at molpro.net
Cc: Ross Nobes
Subject: RE: [molpro-user] Parallel Molpro 2002.6 on ALTIX 350
Hi Ross,
I tried this gmake options as you wrote and I get the following error
during gmake of GA:
IPO Error: unresolved : _fastbcopy
Referenced in libarmci.a(armci.o)
Referenced in libarmci.a(message.o)
Referenced in libarmci.a(mutex.o)
Referenced in libarmci.a(strided.o)
Referenced in libarmci.a(vector.o)
Referenced in libarmci.a(rmw.o)
Referenced in libarmci.a(memlock.o)
Referenced in libarmci.a(request.o)
../../lib/LINUX64/libarmci.a(strided.o)(.text+0x24b2): In function
`armci_copy_2D':
: undefined reference to `_fastbcopy'
../../lib/LINUX64/libarmci.a(strided.o)(.text+0x2532): In function
`armci_copy_2D':
: undefined reference to `_fastbcopy'
../../lib/LINUX64/libarmci.a(strided.o)(.text+0x2572): In function
`armci_copy_2D':
: undefined reference to `_fastbcopy'
../../lib/LINUX64/libarmci.a(strided.o)(.text+0x2632): In function
`armci_copy_2D':
: undefined reference to `_fastbcopy'
../../lib/LINUX64/libarmci.a(strided.o)(.text+0x2692): In function
`armci_copy_2D':
: undefined reference to `_fastbcopy'
../../lib/LINUX64/libarmci.a(strided.o)(.text+0x2712): more undefined
references to `_fastbcopy' follow
gmake[2]: *** [test.x] Error 1
rm util.o ffflush.o test.o
gmake[2]: Leaving directory `/opt/GlobalArray3.3.3/g/global/testing'
gmake[1]: *** [test.x] Error 1
gmake[1]: Leaving directory `/opt/GlobalArray3.3.3/g/global'
gmake: *** [test] Error 2
Did you run into this error?
Thank you
Jacek
Ross wrote------
Hi Jacek,
If you want to use the TCGMSG-based version of the GA, you will need
to
build with
make TARGET=LINUX64 CC=icc FC=ifort
Cheers,
Ross
-----Original Message-----
From: owner-molpro-user at molpro1.chem.cf.ac.uk [mailto:owner-molpro-
user at molpro1.chem.cf.ac.uk] On Behalf Of Jacek Klos
Sent: 14 September 2005 17:28
To: molpro-user at molpro.net
Subject: [molpro-user] Parallel Molpro 2002.6 on ALTIX 350
Dear Molpro users,
I am trying to install parallel version of molpro 2002.6
on SGI ALTIX 350 Itanium2 system with NUMAlink interconnect.
I use ifort 9 and icc 9 Intel compiler. I succesfully compiled
and linked serial version of Molpro, but I run into problems
with parallel version.
I am seeking advise on how to properly compile Global Arrays
and link it with Molpro installation. If I compile GA
using TARGET=LINUX it compiles, but molpro linker fails
with a lot of unresolved symbols, for example:
IPO Error: unresolved : pbeginf_
Referenced in libmolpro.a(mpputil.o)
IPO Error: unresolved : mitob_
Referenced in libmolpro.a(mpputil.o)
Referenced in libmolpro.a(globalop.o)
IPO Error: unresolved : pend_
Referenced in libmolpro.a(mpputil.o)
IPO Error: unresolved : nodeid_
Referenced in libmolpro.a(mpputil.o)
IPO Error: unresolved : nnodes_
Referenced in libmolpro.a(mpputil.o)
IPO Error: unresolved : mdtob_
Referenced in libmolpro.a(mpputil.o)
Referenced in libmolpro.a(globalop.o)
Referenced in libmolpro.a(getbs.o)
/opt/GlobalArray3.3.3/g/lib/LINUX/libarmci.a(fence.o)(.text+0xaa1): In
function `ARMCI_Barrier':
: undefined reference to `SYNCH_'
/opt/GlobalArray3.3.3/g/lib/LINUX/libarmci.a(message.o)(.text+0x15a2):
In
function `armci_msg_barrier':
_sbuf/message.c:377: undefined reference to `SYNCH_'
/opt/GlobalArray3.3.3/g/lib/LINUX/libarmci.a(message.o)(.text+0x15f2):
In
function `armci_msg_me':
_sbuf/message.c:391: undefined reference to `NODEID_'
/opt/GlobalArray3.3.3/g/lib/LINUX/libarmci.a(message.o)(.text+0x1652):
In
function `armci_msg_nproc':
_sbuf/message.c:405: undefined reference to `NNODES_'
/opt/GlobalArray3.3.3/g/lib/LINUX/libarmci.a(message.o)(.text+0x16b2):
In
function `armci_timer':
_sbuf/message.c:419: undefined reference to `tcgtime_'
/opt/GlobalArray3.3.3/g/lib/LINUX/libarmci.a(message.o)(.text+0x1752):
In
function `armci_msg_abort':
and so on.
I think my GA installation is not full and I will be glad to hear from
experts in this matter.
Thank you in advance
Jacek
Jacek A. Klos
---------------------------------
Quantum Chemistry Laboratory |
Department of Chemistry |
University of Warsaw |
Pasteura 1 Street |
02-093 Warsaw |
Poland |
(+4822)8220211 ext. 213 |
e-mail: jakl at tiger.chem.uw.edu.pl|
---------------------------------
Jacek A. Klos
---------------------------------
Quantum Chemistry Laboratory |
Department of Chemistry |
University of Warsaw |
Pasteura 1 Street |
02-093 Warsaw |
Poland |
(+4822)8220211 ext. 213 |
e-mail: jakl at tiger.chem.uw.edu.pl|
---------------------------------
Jacek A. Klos
---------------------------------
Quantum Chemistry Laboratory |
Department of Chemistry |
University of Warsaw |
Pasteura 1 Street |
02-093 Warsaw |
Poland |
(+4822)8220211 ext. 213 |
e-mail: jakl at tiger.chem.uw.edu.pl|
---------------------------------
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