Recompile AMICA on Ubuntu using Intel OneAPI

[tiborauer]

Could you please provide more specific instructions on how to recompile AMICA on Ubuntu using Intel OneAPI? I am afraid the wiki saying "Try using Intel OneAPI modifiying the commands similar to the instructions for Windows above" did not help.

[japalmer29]

Could you provide the compile command you used and the error messages you got (orna summary if they are excessive)?

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________________________________ From: Tibor Auer ***@***.***> Sent: Monday, February 24, 2025 8:24:52 AM To: sccn/amica ***@***.***> Cc: Subscribed ***@***.***> Subject: [sccn/amica] Recompile AMICA on Ubuntu using Intel OneAPI (Issue #49) Could you please provide more specific instructions on how to recompile AMICA on Ubuntu using Intel OneAPI? I am afraid the wiki<https://github.com/sccn/amica/wiki/AMICA-Compilation-instructions> saying "Try using Intel OneAPI modifiying the commands similar to the instructions for Windows above" did not help. — Reply to this email directly, view it on GitHub<#49>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESQJMDDKXU7PUUVZJBL2RMMSJAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43ASLTON2WKOZSHA3TIOJWGAZDKMY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> [tiborauer]tiborauer created an issue (sccn/amica#49)<#49> Could you please provide more specific instructions on how to recompile AMICA on Ubuntu using Intel OneAPI? I am afraid the wiki<https://github.com/sccn/amica/wiki/AMICA-Compilation-instructions> saying "Try using Intel OneAPI modifiying the commands similar to the instructions for Windows above" did not help. — Reply to this email directly, view it on GitHub<#49>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESQJMDDKXU7PUUVZJBL2RMMSJAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43ASLTON2WKOZSHA3TIOJWGAZDKMY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[tiborauer]

I tried different thigs:
mpif90 -I/opt/intel/oneapi/mkl/latest/include -fpp -fopenmp -mkl -DMKL -O3 funmod2.f90 amica15.f90 amica15ub_2
gfortran: error: unrecognized command-line option \u2018-fpp\u2019; did you mean \u2018-cpp\u2019?

mpif90 -I/opt/intel/oneapi/mkl/latest/include -cpp -fopenmp -mkl -DMKL -O3 funmod2.f90 amica15.f90 amica15ub_2
amica15_header.f90:33:132:

33 | :,:), Stmp(:,:), Stmp2(:,:), Stmp3(:,:), dWtmp(:,:,:), ipivnx(:), ipivnw(:)
| 1

Error: Line truncated at (1) [-Werror=line-truncation]
amica15_header.f90:53:132:

53 | ralpha_denom_tmp(:,:,:), dbaralpha_numer(:,:,:), dbaralpha_denom(:,:,:)
| 1

Error: Line truncated at (1) [-Werror=line-truncation]
amica15_header.f90:53:132:

53 | ralpha_denom_tmp(:,:,:), dbaralpha_numer(:,:,:), dbaralpha_denom(:,:,:)
| 1

Error: Missing \u2018)\u2019 in statement at or before (1)
...

[japalmer29]

That indicates it's using gfortran, not Intel. Tou need to find the batch script for your processor (32 or 64 bit) and run that at a command prompt. That will set the paths so that mpif90 calls ifort bot gfortran.

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________________________________ From: Tibor Auer ***@***.***> Sent: Monday, February 24, 2025 11:42:30 AM To: sccn/amica ***@***.***> Cc: Jason Palmer ***@***.***>; Comment ***@***.***> Subject: Re: [sccn/amica] Recompile AMICA on Ubuntu using Intel OneAPI (Issue #49) I tried different thigs: mpif90 -I/opt/intel/oneapi/mkl/latest/include -fpp -fopenmp -mkl -DMKL -O3 funmod2.f90 amica15.f90 amica15ub_2 gfortran: error: unrecognized command-line option \u2018-fpp\u2019; did you mean \u2018-cpp\u2019? — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESX75P56WHV4WVI4GZT2RNDXNAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGA2DCNJZHA>. You are receiving this because you commented.Message ID: ***@***.***> [tiborauer]tiborauer left a comment (sccn/amica#49)<#49 (comment)> I tried different thigs: mpif90 -I/opt/intel/oneapi/mkl/latest/include -fpp -fopenmp -mkl -DMKL -O3 funmod2.f90 amica15.f90 amica15ub_2 gfortran: error: unrecognized command-line option \u2018-fpp\u2019; did you mean \u2018-cpp\u2019? — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESX75P56WHV4WVI4GZT2RNDXNAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGA2DCNJZHA>. You are receiving this because you commented.Message ID: ***@***.***>

[tiborauer]

What batch script? Where can I find it?

[japalmer29]

I don't recall exactly but scripts are under something like compilervars or compile something. Then under Intel32 or intel64 or a mac equivalents you'll find scripts that set paths. Check that mpf90 links to an Intel path not gfortran.

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________________________________ From: Jason Palmer ***@***.***> Sent: Monday, February 24, 2025 11:45:59 AM To: sccn/amica ***@***.***>; sccn/amica ***@***.***> Cc: Comment ***@***.***> Subject: Re: [sccn/amica] Recompile AMICA on Ubuntu using Intel OneAPI (Issue #49) That indicates it's using gfortran, not Intel. Tou need to find the batch script for your processor (32 or 64 bit) and run that at a command prompt. That will set the paths so that mpif90 calls ifort bot gfortran.

________________________________ From: Tibor Auer ***@***.***> Sent: Monday, February 24, 2025 11:42:30 AM To: sccn/amica ***@***.***> Cc: Jason Palmer ***@***.***>; Comment ***@***.***> Subject: Re: [sccn/amica] Recompile AMICA on Ubuntu using Intel OneAPI (Issue #49) I tried different thigs: mpif90 -I/opt/intel/oneapi/mkl/latest/include -fpp -fopenmp -mkl -DMKL -O3 funmod2.f90 amica15.f90 amica15ub_2 gfortran: error: unrecognized command-line option \u2018-fpp\u2019; did you mean \u2018-cpp\u2019? — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESX75P56WHV4WVI4GZT2RNDXNAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGA2DCNJZHA>. You are receiving this because you commented.Message ID: ***@***.***> [tiborauer]tiborauer left a comment (sccn/amica#49)<#49 (comment)> I tried different thigs: mpif90 -I/opt/intel/oneapi/mkl/latest/include -fpp -fopenmp -mkl -DMKL -O3 funmod2.f90 amica15.f90 amica15ub_2 gfortran: error: unrecognized command-line option \u2018-fpp\u2019; did you mean \u2018-cpp\u2019? — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESX75P56WHV4WVI4GZT2RNDXNAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGA2DCNJZHA>. You are receiving this because you commented.Message ID: ***@***.***>

[tiborauer]

I found this: /opt/intel/oneapi/setvars.sh

[japalmer29]

Look in the install directory for OneAPI.

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________________________________ From: Jason Palmer ***@***.***> Sent: Monday, February 24, 2025 11:50:33 AM To: sccn/amica ***@***.***>; sccn/amica ***@***.***> Cc: Comment ***@***.***> Subject: Re: [sccn/amica] Recompile AMICA on Ubuntu using Intel OneAPI (Issue #49) I don't recall exactly but scripts are under something like compilervars or compile something. Then under Intel32 or intel64 or a mac equivalents you'll find scripts that set paths. Check that mpf90 links to an Intel path not gfortran.

________________________________ From: Jason Palmer ***@***.***> Sent: Monday, February 24, 2025 11:45:59 AM To: sccn/amica ***@***.***>; sccn/amica ***@***.***> Cc: Comment ***@***.***> Subject: Re: [sccn/amica] Recompile AMICA on Ubuntu using Intel OneAPI (Issue #49) That indicates it's using gfortran, not Intel. Tou need to find the batch script for your processor (32 or 64 bit) and run that at a command prompt. That will set the paths so that mpif90 calls ifort bot gfortran.

________________________________ From: Tibor Auer ***@***.***> Sent: Monday, February 24, 2025 11:42:30 AM To: sccn/amica ***@***.***> Cc: Jason Palmer ***@***.***>; Comment ***@***.***> Subject: Re: [sccn/amica] Recompile AMICA on Ubuntu using Intel OneAPI (Issue #49) I tried different thigs: mpif90 -I/opt/intel/oneapi/mkl/latest/include -fpp -fopenmp -mkl -DMKL -O3 funmod2.f90 amica15.f90 amica15ub_2 gfortran: error: unrecognized command-line option \u2018-fpp\u2019; did you mean \u2018-cpp\u2019? — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESX75P56WHV4WVI4GZT2RNDXNAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGA2DCNJZHA>. You are receiving this because you commented.Message ID: ***@***.***> [tiborauer]tiborauer left a comment (sccn/amica#49)<#49 (comment)> I tried different thigs: mpif90 -I/opt/intel/oneapi/mkl/latest/include -fpp -fopenmp -mkl -DMKL -O3 funmod2.f90 amica15.f90 amica15ub_2 gfortran: error: unrecognized command-line option \u2018-fpp\u2019; did you mean \u2018-cpp\u2019? — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESX75P56WHV4WVI4GZT2RNDXNAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGA2DCNJZHA>. You are receiving this because you commented.Message ID: ***@***.***>

[japalmer29]

Try it, and then "which mpif90". It should point to a compiler in the oneapi path.

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________________________________ From: Tibor Auer ***@***.***> Sent: Monday, February 24, 2025 11:51:39 AM To: sccn/amica ***@***.***> Cc: Jason Palmer ***@***.***>; Comment ***@***.***> Subject: Re: [sccn/amica] Recompile AMICA on Ubuntu using Intel OneAPI (Issue #49) I found this: /opt/intel/oneapi/setvars.sh — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESQSO6SW74GOMPUQ5EL2RNEZXAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGA3DQMJXGQ>. You are receiving this because you commented.Message ID: ***@***.***> [tiborauer]tiborauer left a comment (sccn/amica#49)<#49 (comment)> I found this: /opt/intel/oneapi/setvars.sh — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESQSO6SW74GOMPUQ5EL2RNEZXAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGA3DQMJXGQ>. You are receiving this because you commented.Message ID: ***@***.***>

[tiborauer]

tibor@fujitsu-1:/home/akk/tools/eeglab/plugins/AMICA1.7$ which mpif90
/opt/intel/oneapi/mpi/2021.14/bin/mpif90

tibor@fujitsu-1:/home/akk/tools/eeglab/plugins/AMICA1.7$ ls /opt/intel/oneapi/mpi/2021.14/bin
cpuinfo IMB-MPI1-GPU impi_cpuinfo mpiexec.hydra mpigxx mpiifort
hydra_bstrap_proxy IMB-MT impi_info mpif77 mpiicc mpiifx
hydra_nameserver IMB-NBC mpicc mpif90 mpiicpc mpirun
hydra_pmi_proxy IMB-P2P mpicxx mpifc mpiicpx mpitune_fast
IMB-MPI1 IMB-RMA mpiexec mpigcc mpiicx

[japalmer29]

Now that the paths are set, go to the amica directory and try the mpif90 compile command.

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________________________________ From: Tibor Auer ***@***.***> Sent: Monday, February 24, 2025 11:55:45 AM To: sccn/amica ***@***.***> Cc: Jason Palmer ***@***.***>; Comment ***@***.***> Subject: Re: [sccn/amica] Recompile AMICA on Ubuntu using Intel OneAPI (Issue #49) ***@***.***:/home/akk/tools/eeglab/plugins/AMICA1.7$ which mpif90 /opt/intel/oneapi/mpi/2021.14/bin/mpif90 ***@***.***:/home/akk/tools/eeglab/plugins/AMICA1.7$ ls /opt/intel/oneapi/mpi/2021.14/bin cpuinfo IMB-MPI1-GPU impi_cpuinfo mpiexec.hydra mpigxx mpiifort hydra_bstrap_proxy IMB-MT impi_info mpif77 mpiicc mpiifx hydra_nameserver IMB-NBC mpicc mpif90 mpiicpc mpirun hydra_pmi_proxy IMB-P2P mpicxx mpifc mpiicpx mpitune_fast IMB-MPI1 IMB-RMA mpiexec mpigcc mpiicx — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESRSJ32YYJ6DVPCKSM32RNFJDAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGA4DIMJTG4>. You are receiving this because you commented.Message ID: ***@***.***> [tiborauer]tiborauer left a comment (sccn/amica#49)<#49 (comment)> ***@***.***:/home/akk/tools/eeglab/plugins/AMICA1.7$ which mpif90 /opt/intel/oneapi/mpi/2021.14/bin/mpif90 ***@***.***:/home/akk/tools/eeglab/plugins/AMICA1.7$ ls /opt/intel/oneapi/mpi/2021.14/bin cpuinfo IMB-MPI1-GPU impi_cpuinfo mpiexec.hydra mpigxx mpiifort hydra_bstrap_proxy IMB-MT impi_info mpif77 mpiicc mpiifx hydra_nameserver IMB-NBC mpicc mpif90 mpiicpc mpirun hydra_pmi_proxy IMB-P2P mpicxx mpifc mpiicpx mpitune_fast IMB-MPI1 IMB-RMA mpiexec mpigcc mpiicx — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESRSJ32YYJ6DVPCKSM32RNFJDAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGA4DIMJTG4>. You are receiving this because you commented.Message ID: ***@***.***>

[tiborauer]

I have run /opt/intel/oneapi/setvars.sh, but mpf90 still uses gfortran

[japalmer29]

Did you run which mpif90 before running mpif90? In what you pasted it pointed to the oneapi path, so I don't see how it is still running gfortran, unless there is an issue woth the oneapi installation.

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________________________________ From: Tibor Auer ***@***.***> Sent: Monday, February 24, 2025 12:01:03 PM To: sccn/amica ***@***.***> Cc: Jason Palmer ***@***.***>; Comment ***@***.***> Subject: Re: [sccn/amica] Recompile AMICA on Ubuntu using Intel OneAPI (Issue #49) I have run /opt/intel/oneapi/setvars.sh, but mpf90 still uses gfortran — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESTXPAG3A32GWZF7XND2RNF47AVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGA4TQMJTGM>. You are receiving this because you commented.Message ID: ***@***.***> [tiborauer]tiborauer left a comment (sccn/amica#49)<#49 (comment)> I have run /opt/intel/oneapi/setvars.sh, but mpf90 still uses gfortran — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESTXPAG3A32GWZF7XND2RNF47AVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGA4TQMJTGM>. You are receiving this because you commented.Message ID: ***@***.***>

[tiborauer]

I only installed this: https://www.intel.com/content/www/us/en/docs/oneapi/installation-guide-linux/2025-0/intel-fortran-essentials.html

[tiborauer]

/opt/intel/oneapi/mpi/2021.14/bin/mpif90 has a line 127 saying FC="gfortran". So it seems I have to use some flag to set ifortran...

[japalmer29]

There are multiple installs you have to do. There is the "base" which installs ifort. Then the hpc which installs the mpi etc.

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________________________________ From: Tibor Auer ***@***.***> Sent: Monday, February 24, 2025 12:19:17 PM To: sccn/amica ***@***.***> Cc: Jason Palmer ***@***.***>; Comment ***@***.***> Subject: Re: [sccn/amica] Recompile AMICA on Ubuntu using Intel OneAPI (Issue #49) /opt/intel/oneapi/mpi/2021.14/bin/mpif90 has a line 127 saying FC="gfortran". So it seems I have to use some flag to set ifortran... — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESRF33BER5W3UKIPLX32RNIBLAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGE2TCMZWGA>. You are receiving this because you commented.Message ID: ***@***.***> [tiborauer]tiborauer left a comment (sccn/amica#49)<#49 (comment)> /opt/intel/oneapi/mpi/2021.14/bin/mpif90 has a line 127 saying FC="gfortran". So it seems I have to use some flag to set ifortran... — Reply to this email directly, view it on GitHub<#49 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACRBESRF33BER5W3UKIPLX32RNIBLAVCNFSM6AAAAABXYAYZ2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZZGE2TCMZWGA>. You are receiving this because you commented.Message ID: ***@***.***>