topic According to the linker in Intel® oneAPI Math Kernel Library

MPICH3 and libmkl_blacs_mpich_

Jesse_Q_ — Sat, 07 Apr 2018 14:32:09 GMT

While attempting to run siesta-4.1-b3 using MPICH3 (3.1.4) with intel mkl 2018 libmkl_blacs_mpich I received the following error:

[Jesses-iMac-2:98886] *** An error occurred in MPI_Comm_rank

[Jesses-iMac-2:98886] *** reported by process [128122881,206158430208]

[Jesses-iMac-2:98886] *** on communicator MPI_COMM_WORLD

[Jesses-iMac-2:98886] *** MPI_ERR_COMM: invalid communicator

[Jesses-iMac-2:98886] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,

[Jesses-iMac-2:98886] *** and potentially your MPI job)

I believe this to be an error with the mpi.h. Is MPICH3 supported or do I need to install MPICH2 (1.5-rc3, latest version I'm aware of for MPICH2)? My operating system is high Sierra OSX.

Hi Jesse,

Ying_H_Intel — Sun, 08 Apr 2018 01:06:43 GMT

Hi Jesse,

Here is the MKL system requirement https://software.intel.com/en-us/articles/intel-math-kernel-library-intel-mkl-2018-system-requirements for your reference.
macOS* 10.12 (Xcode 8.x) and macOS* 10.13 (Xcode 9.x) (Intel® 64)
MPICH version 3.1 (http://www-unix.mcs.anl.gov/mpi/mpich) is supported

What is compiler on that machine?

One more thing, the zip file you shared seems empty

Best Regards,
Ying

P.S https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/
which will help to provide the exact MKL library wanted when you link in application.

for example, -qopenmp $(MKL)/lib/libmkl_blas95_ilp64.a $(MKL)/lib/libmkl_lapack95_ilp64.a $(INTEL_LIBS) -Wl,-rpath,$(MKL)/lib \
-lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_mpich_ilp64 -liomp5 -lpthread -lm -ldl

Here you are using the ILP64 (integer is 64bit). Please make sure your siesta application ask the 64bit integer.

Hi Ying,

Jesse_Q_ — Sun, 08 Apr 2018 09:29:17 GMT

Hi Ying,

My compilers are version 18.0.2 and xcode 9.3.

I will redo all compilations (hdf5, netcdf, netcdf-fortran) with mpich 3.1 (mpich-3.1.tar.gz) and will link with 32 bit and 64 bit to see if that is also a problem. I will get back to you shortly.

Regards,

OK.

Jesse_Q_ — Sun, 08 Apr 2018 22:10:49 GMT

OK.

Compiling with Mpich3.1 either 64/32 int I get the following error

[jessequinn@Jesses-iMac-2 Tests]$ make MPI="mpirun -np 4 /Users/jessequinn/Packages/tmp/siesta-4.1-b3/Obj/siesta"

/Applications/Xcode.app/Contents/Developer/usr/bin/make -C ag completed

>>>> Running ag test...

==> Copying pseudopotential file for Ag...

==> Running SIESTA as mpirun -np 4 /Users/jessequinn/Packages/tmp/siesta-4.1-b3/Obj/siesta ../../../siesta -fdf XML.Write ../ag.fdf

forrtl: severe (174): SIGSEGV, segmentation fault occurred

Image PC Routine Line Source

libifcoremt.dylib 000000010D6D5254 for__signal_handl Unknown Unknown

libsystem_platfor 00007FFF7D032F5A _sigtramp Unknown Unknown

libmpi.40.dylib 000000010D167204 MPI_Comm_rank Unknown Unknown

libpmpich.12.dyli 000000010D25356B mpi_comm_rank_ Unknown Unknown

siesta 0000000102BAE3B5 mpi_siesta_mp_mym Unknown Unknown

siesta 000000010247A6B2 m_siesta_init_mp_ Unknown Unknown

siesta 0000000102ABDA70 MAIN__ Unknown Unknown

siesta 0000000102234DAE main Unknown Unknown

forrtl: severe (174): SIGSEGV, segmentation fault occurred

Image PC Routine Line Source

libifcoremt.dylib 0000000115E07254 for__signal_handl Unknown Unknown

libsystem_platfor 00007FFF7D032F5A _sigtramp Unknown Unknown

libmpi.40.dylib 00000001112CC204 MPI_Comm_rank Unknown Unknown

libpmpich.12.dyli 00000001159CE56B mpi_comm_rank_ Unknown Unknown

siesta 000000010B20B3B5 mpi_siesta_mp_mym Unknown Unknown

siesta 000000010AAD76B2 m_siesta_init_mp_ Unknown Unknown

siesta 000000010B11AA70 MAIN__ Unknown Unknown

siesta 000000010A891DAE main Unknown Unknown

forrtl: severe (174): SIGSEGV, segmentation fault occurred

Image PC Routine Line Source

libifcoremt.dylib 000000010BD78254 for__signal_handl Unknown Unknown

libsystem_platfor 00007FFF7D032F5A _sigtramp Unknown Unknown

libmpi.40.dylib 000000010AD75204 MPI_Comm_rank Unknown Unknown

libpmpich.12.dyli 000000010B93F56B mpi_comm_rank_ Unknown Unknown

siesta 00000001011743B5 mpi_siesta_mp_mym Unknown Unknown

siesta 0000000100A406B2 m_siesta_init_mp_ Unknown Unknown

siesta 0000000101083A70 MAIN__ Unknown Unknown

siesta 00000001007FADAE main Unknown Unknown

forrtl: severe (174): SIGSEGV, segmentation fault occurred

Image PC Routine Line Source

libifcoremt.dylib 00000001148D9254 for__signal_handl Unknown Unknown

libsystem_platfor 00007FFF7D032F5A _sigtramp Unknown Unknown

libmpi.40.dylib 000000011438A204 MPI_Comm_rank Unknown Unknown

libpmpich.12.dyli 000000011446756B mpi_comm_rank_ Unknown Unknown

siesta 00000001106A83B5 mpi_siesta_mp_mym Unknown Unknown

siesta 000000010FF746B2 m_siesta_init_mp_ Unknown Unknown

siesta 00000001105B7A70 MAIN__ Unknown Unknown

siesta 000000010FD2EDAE main Unknown Unknown

make[1]: *** [completed_work] Error 174

make: *** [ag] Error 2

[jessequinn@Jesses-iMac-2 Tests]$

Any idea?

Hi Jesse,

Ying_H_Intel — Mon, 09 Apr 2018 03:17:56 GMT

Hi Jesse,

Do you have other machine like Linux etc? the MPI and Mac OS maybe still issue.

From system requirement, it seems not MPI for Mac OS.

MPI implementations that Intel® MKL for Windows* OS has been validated against:

Intel® MPI Library Version 5.1 (Intel® 64) (http://www.intel.com/go/mpi)
Intel® MPI Library Version 2018 (Intel® 64) (http://www.intel.com/go/mpi)
Intel® MPI Library Version 2017 (Intel® 64) (http://www.intel.com/go/mpi)
MPICH2 version 1.5 (http://www-unix.mcs.anl.gov/mpi/mpich)
MS MPI, CCE or HPC 2012 on Intel® 64 (http://www.microsoft.com/downloads)
Open MPI 1.8.x (Intel® 64) (http://www.open-mpi.org)

MPI implementations that Intel® MKL for Linux* OS has been validated against:

Intel® MPI Library Version 5.1 (Intel® 64) (http://www.intel.com/go/mpi)
Intel® MPI Library Version 2018 (Intel® 64) (http://www.intel.com/go/mpi)
Intel® MPI Library Version 2017 (Intel® 64) (http://www.intel.com/go/mpi)
MPICH2 version 1.5 (Intel® 64) (http://www-unix.mcs.anl.gov/mpi/mpich)
MPICH version 3.1 (http://www-unix.mcs.anl.gov/mpi/mpich)
MPICH version 3.2 (http://www-unix.mcs.anl.gov/mpi/mpich)
Open MPI 1.8.x (Intel® 64) (http://www.open-mpi.org)

Or the environment and dependency seems complex. Could you submit your question to On-line sever center supporttickets.intel.com/ where our engineer may help to see the details.

Best Regards,

Ying

According to the linker

Jesse_Q_ — Mon, 09 Apr 2018 11:25:12 GMT

According to the linker

MPICH is the only MPI implementation supported. However, what version I do not know!!! And no, I do not have a linux.

Hi Jesse,

Konstantin_A_Intel — Wed, 25 Apr 2018 20:54:49 GMT

Hi Jesse,

As I can see, Siesta crashes at the initialization stage during MPI_Comm_rank. That indicates that you definitely have some issues with MPI and it is hardly connected to MKL. So, I recommend you either to try MPICH 2 or to run a simple MPI test first.

Regards,

Konstantin