topic Hello Comput, in Intel® oneAPI Math Kernel Library

Link errors for MKL function from mkl_scalapack.h with C++

comput — Mon, 30 Jul 2018 16:23:55 GMT

Hello,
I hope you could help please in this problem.
I try to compile a small C++ function that calls the MKL function "pdgesvd" from the header "mkl_scalapack.h".
The C++ code is:

#include "mkl_scalapack.h"
int main()
{
// defining the variables ...

   pdgesvd(jobu, jobvt, m, n,
           a, ia, ja, desca,
           s, u, iu, ju, descu,
           vt, ivt, jvt, descvt,
           work, lwork, info);

return 0;
}

The link fails with the errors in the attached file "link_errors.pdf".

I have run the script:
source /intel/bin/compilervars.sh -arch intel64 -platform linux

I got the compilation/link options from the online "Intel® Math Kernel Library Link Line Advisor" (the options attached in the snapshot intel_advisor.jpg) and compiling as below:

g++ -O main.cpp \
-DMKL_ILP64 -m64 -I${MKLROOT}/include \
${MKLROOT}/lib/intel64/libmkl_scalapack_ilp64.a -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_cdft_core.a ${MKLROOT}/lib/intel64/libmkl_intel_ilp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_blacs_intelmpi_ilp64.a -Wl,--end-group -liomp5 -lpthread -lm -ldl

I would appreciate any assistance,

Thank you.

Hi Comput,

Ying_H_Intel — Tue, 31 Jul 2018 01:03:56 GMT

Hi Comput,

The link errors are mainly MPI related symbols. You can resolve them by adding MPI runtime library in the command line. For example, if you use Intel MPI

source /opt/intel/bin/compilervars.sh intel64
source /opt/intel/impi/201x.x.0xx/intel64/bin/mpivars.sh (replace the x with your MPI version)

mpiicc -DMKL_ILP64 -m64 -I${MKLROOT}/include -Wl,--start-group "/opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64"/libmkl_blacs_intelmpi_ilp64.a "/opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64"/libmkl_intel_ilp64.a "/opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64"/libmkl_core.a "/opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64"/libmkl_intel_thread.a -Wl,--end-group -L "/opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/../compiler/lib/intel64" -liomp5 -mt_mpi -lm -ldl

Best Regards,
Ying

Hello Ying,

comput — Tue, 31 Jul 2018 04:47:18 GMT

Hello Ying,
Thank you for your reply.

I tried as you suggested and it compiles now:
source /intel/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpivars.sh
source /intel/bin/compilervars.sh -arch intel64 -platform linux

However the MPI library is dynamic, not static.

I had tried all the above commands (including the mpivars.sh) before posting to the forum, but I had tried linking with the static libmpi_mt.a instead of the dynamic libmpi_mt.so and it was giving link errors. It still gives those link errors with the static MPI library.

Namely, if instead of the dynamic MPI library:
-L/intel/compilers_and_libraries_2018.3.222/linux/mpi/intel64/lib -lmpi_mt

using instead the static one, that gives link errors:
/intel/compilers_and_libraries_2018.3.222/linux/mpi/intel64/lib/libmpi_mt.a
I think this is not important, but I attach anyway those errors in the file "static_mpi_link_errors.pdf" just in case it is useful to know.

It is not a problem for me to use the dynamic MPI library as long as the dynamic MPI library would not give errors on run-time (the same errors with the static MPI library).
From a quick run with all the pointer arguments of the function "pdgesvd" set to zero, it runs without any link errors. Only it gives a segmentation fault, which is expected since the arguments are set to zero at the moment (I need some time to study the arguments from the manual).

I think the problem is solved.
I would let you know if there is any difference on the run-time.

Best regards and thank you very much for your help.

Hello Comput,

Ying_H_Intel — Thu, 02 Aug 2018 01:47:00 GMT

Hello Comput,

You are welcomed. About the static link, for intel mpi . Generally, we use the mpicc xxx -static_mpi and let them to help find needed libraries, include mpi's static librares.

for example, we have mkl cluster sample under mkl install folder (you can test them too).

[yhu5@hsw-ep01 pblasc]$ mpicc -o pblas1_d_example source/pblas1_d_example.c -L/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64 -Wl,--start-group /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_intel_lp64.a /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_sequential.a /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -static_mpi -lpthread -lm -ldl

and if you use gcc directly, then you have to add all needed libraries manually, for example

gcc -o pblas1_d_example source/pblas1_d_example.c -L/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64 -Wl,--start-group /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_intel_lp64.a /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_sequential.a /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread /opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib/libmpi_mt.a /opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib/libmpigi.a /opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib/libmpigf.a /opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib/libmpicxx.a /opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib/libmpigc4.a /opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib/libmpifort.a -lm -ldl -lrt

Best Regards,
Ying

This is useful to know, thank

comput — Tue, 14 Aug 2018 20:28:35 GMT

This is useful to know, thank you.
Best regards,
Compute