Some misc doc for HPC on ARM
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CMAQ: Confusing steps for installing IOAPI
The second and third steps at https://github.com/Yikun/hpc-arm/blob/main/CMAQ.md#compiling-and-installing-cmaq are confusing.
In the first step we download ioapi-3.2-2020111.tar.gz in the current folder (unspecified location). Then we cd to /path/to/CMAQ and try to extract ioapi-3.2-2020111.tar.gz but it is not in the current folder, so we need to use an absolute path instead!
What is even more confusing is that later at step 6 we do export HOME=/path/to/CMAQ, i.e. we override HOME`` for the current user. Why is this needed ? Can't we use CMAQ_HOME` or similar instead ?
Quantum Espresso build fails with devtoolset-9
See my comments at https://github.com/Yikun/hpc-arm/pull/2/files#r688400683
NEMO: Make it more clear what `target_configure` and `your_configure` are
It is not clear what `-r 'target_configure' -n 'your_configure'`` are in:
https://github.com/Yikun/hpc-arm/blame/02995b868db8ccadd8666161b23b5510c6a5f6e9/NEMO.md#L286
NEMO build failure - Xios
See my comment at #4 (comment)
CMAQ: Build failure for ioapi
Following the steps at https://github.com/Yikun/hpc-arm/blob/main/CMAQ.md#compiling-and-installing-cmaq lead to this error:
[root@c31236451db8 ioapi-3.2]# make BIN=Linux4_aarch64
Makefile:273: warning: overriding recipe for target `/path/to/CMAQ/Linux4_aarch64'
Makefile:270: warning: ignoring old recipe for target `/path/to/CMAQ/Linux4_aarch64'
(cd /WRF/ioapi-3.2/ioapi ; make fixed_src)
make[1]: Entering directory `/WRF/ioapi-3.2/ioapi'
make[1]: Nothing to be done for `fixed_src'.
make[1]: Leaving directory `/WRF/ioapi-3.2/ioapi'
(cd /WRF/ioapi-3.2/ioapi ; sed -e 's|IOAPI_BASE|/WRF/ioapi-3.2|' -e 's|LIBINSTALL|/path/to/CMAQ/Linux4_aarch64|' -e 's|BININSTALL|/path/to/CMAQ/Linux4_aarch64|' -e 's|IOAPI_DEFS|"-DIOAPI_NCF4"|' -e 's|NCFLIBS|-L/path/to/NETCDF/lib -lnetcdff -lnetcdf -L/path/to/HDF5/lib -lhdf5_hl -lhdf5 -lz|' -e 's|MAKEINCLUDE|include /WRF/ioapi-3.2/ioapi/Makeinclude|' -e 's|PVMINCLUDE|include |' < Makefile.nocpl.sed > Makefile )
(cd /WRF/ioapi-3.2/m3tools ; sed -e 's|IOAPI_BASE|/WRF/ioapi-3.2|' -e 's|LIBINSTALL|/path/to/CMAQ/Linux4_aarch64|' -e 's|BININSTALL|/path/to/CMAQ/Linux4_aarch64|' -e 's|IOAPI_DEFS|"-DIOAPI_NCF4"|' -e 's|NCFLIBS|-L/path/to/NETCDF/lib -lnetcdff -lnetcdf -L/path/to/HDF5/lib -lhdf5_hl -lhdf5 -lz|' -e 's|MAKEINCLUDE|include /WRF/ioapi-3.2/ioapi/Makeinclude|' -e 's|PVMINCLUDE|include |' < Makefile.nocpl.sed > Makefile )
(cd /WRF/ioapi-3.2/ioapi ; make BIN=Linux4_aarch64 all)
make[1]: Entering directory `/WRF/ioapi-3.2/ioapi'
cd /WRF/ioapi-3.2/Linux4_aarch64; mpifort -c -DAUTO_ARRAYS=1 -DF90=1 -DFLDMN=1 -DFSTR_L=int -DIOAPI_NO_STDOUT=1 -DNEED_ARGS=1 -O3 -ffast-math -funroll-loops -fopenmp -DAUTO_ARRAYS=1 -DF90=1 -DFLDMN=1 -DFSTR_L=int -DIOAPI_NO_STDOUT=1 -DNEED_ARGS=1 -I/WRF/ioapi-3.2/ioapi /WRF/ioapi-3.2/ioapi/modwrfio.f90
cd /WRF/ioapi-3.2/Linux4_aarch64; mpifort -c -DAUTO_ARRAYS=1 -DF90=1 -DFLDMN=1 -DFSTR_L=int -DIOAPI_NO_STDOUT=1 -DNEED_ARGS=1 -O3 -ffast-math -funroll-loops -fopenmp -DAUTO_ARRAYS=1 -DF90=1 -DFLDMN=1 -DFSTR_L=int -DIOAPI_NO_STDOUT=1 -DNEED_ARGS=1 -I/WRF/ioapi-3.2/ioapi /WRF/ioapi-3.2/ioapi/modmpasfio.f90
cd /WRF/ioapi-3.2/Linux4_aarch64; mpifort -c -DF90=1 -DAUTO_ARRAYS=1 -DF90=1 -DFLDMN=1 -DFSTR_L=int -DIOAPI_NO_STDOUT=1 -DNEED_ARGS=1 -O3 -ffast-math -funroll-loops -fopenmp -DAUTO_ARRAYS=1 -DF90=1 -DFLDMN=1 -DFSTR_L=int -DIOAPI_NO_STDOUT=1 -DNEED_ARGS=1 -I/WRF/ioapi-3.2/ioapi /WRF/ioapi-3.2/ioapi/modpdata.F90
cd /WRF/ioapi-3.2/Linux4_aarch64; mpifort -c -DF90=1 -DAUTO_ARRAYS=1 -DF90=1 -DFLDMN=1 -DFSTR_L=int -DIOAPI_NO_STDOUT=1 -DNEED_ARGS=1 -O3 -ffast-math -funroll-loops -fopenmp -DAUTO_ARRAYS=1 -DF90=1 -DFLDMN=1 -DFSTR_L=int -DIOAPI_NO_STDOUT=1 -DNEED_ARGS=1 -I/WRF/ioapi-3.2/ioapi /WRF/ioapi-3.2/ioapi/modatts3.F90
cd /WRF/ioapi-3.2/Linux4_aarch64; mpifort -c -DF90=1 -DAUTO_ARRAYS=1 -DF90=1 -DFLDMN=1 -DFSTR_L=int -DIOAPI_NO_STDOUT=1 -DNEED_ARGS=1 -O3 -ffast-math -funroll-loops -fopenmp -DAUTO_ARRAYS=1 -DF90=1 -DFLDMN=1 -DFSTR_L=int -DIOAPI_NO_STDOUT=1 -DNEED_ARGS=1 -I/WRF/ioapi-3.2/ioapi /WRF/ioapi-3.2/ioapi/modncfio.F90
/WRF/ioapi-3.2/ioapi/modncfio.F90:16601:60:
16601 | ISTAT = NF_PUT_VARA_DOUBLE( FID, VID, DIMS, DELS, GRID )
| 1
......
19612 | ISTAT = NF_PUT_VARA_DOUBLE( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:16493:58:
16493 | ISTAT = NF_PUT_VARA_INT1( FID, VID, DIMS, DELS, GRID )
| 1
......
19436 | ISTAT = NF_PUT_VARA_INT1( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:16385:58:
16385 | ISTAT = NF_PUT_VARA_INT2( FID, VID, DIMS, DELS, GRID )
| 1
......
19260 | ISTAT = NF_PUT_VARA_INT2( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:16277:57:
16277 | ISTAT = NF_PUT_VARA_INT( FID, VID, DIMS, DELS, GRID )
| 1
......
19084 | ISTAT = NF_PUT_VARA_INT( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:16169:58:
16169 | ISTAT = NF_PUT_VARA_REAL( FID, VID, DIMS, DELS, GRID )
| 1
......
18908 | ISTAT = NF_PUT_VARA_REAL( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:11321:60:
11321 | ISTAT = NF_PUT_VARA_DOUBLE( FID, VID, DIMS, DELS, GRID )
| 1
......
19612 | ISTAT = NF_PUT_VARA_DOUBLE( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:11229:58:
11229 | ISTAT = NF_PUT_VARA_INT1( FID, VID, DIMS, DELS, GRID )
| 1
......
19436 | ISTAT = NF_PUT_VARA_INT1( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:11137:58:
11137 | ISTAT = NF_PUT_VARA_INT2( FID, VID, DIMS, DELS, GRID )
| 1
......
19260 | ISTAT = NF_PUT_VARA_INT2( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:11045:57:
11045 | ISTAT = NF_PUT_VARA_INT( FID, VID, DIMS, DELS, GRID )
| 1
......
19084 | ISTAT = NF_PUT_VARA_INT( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:10953:58:
10953 | ISTAT = NF_PUT_VARA_REAL( FID, VID, DIMS, DELS, GRID )
| 1
......
18908 | ISTAT = NF_PUT_VARA_REAL( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:7850:60:
7850 | ISTAT = NF_GET_VARA_DOUBLE( FID, VID, DIMS, DELS, GRID )
| 1
......
10861 | ISTAT = NF_GET_VARA_DOUBLE( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:7742:58:
7742 | ISTAT = NF_GET_VARA_INT1( FID, VID, DIMS, DELS, GRID )
| 1
......
10685 | ISTAT = NF_GET_VARA_INT1( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:7634:58:
7634 | ISTAT = NF_GET_VARA_INT2( FID, VID, DIMS, DELS, GRID )
| 1
......
10509 | ISTAT = NF_GET_VARA_INT2( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:7526:57:
7526 | ISTAT = NF_GET_VARA_INT( FID, VID, DIMS, DELS, GRID )
| 1
......
10333 | ISTAT = NF_GET_VARA_INT( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:7418:58:
7418 | ISTAT = NF_GET_VARA_REAL( FID, VID, DIMS, DELS, GRID )
| 1
......
10157 | ISTAT = NF_GET_VARA_REAL( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:2570:60:
2570 | ISTAT = NF_GET_VARA_DOUBLE( FID, VID, DIMS, DELS, GRID )
| 1
......
10861 | ISTAT = NF_GET_VARA_DOUBLE( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:2478:58:
2478 | ISTAT = NF_GET_VARA_INT1( FID, VID, DIMS, DELS, GRID )
| 1
......
10685 | ISTAT = NF_GET_VARA_INT1( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:2386:58:
2386 | ISTAT = NF_GET_VARA_INT2( FID, VID, DIMS, DELS, GRID )
| 1
......
10509 | ISTAT = NF_GET_VARA_INT2( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:2294:57:
2294 | ISTAT = NF_GET_VARA_INT( FID, VID, DIMS, DELS, GRID )
| 1
......
10333 | ISTAT = NF_GET_VARA_INT( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
/WRF/ioapi-3.2/ioapi/modncfio.F90:2202:58:
2202 | ISTAT = NF_GET_VARA_REAL( FID, VID, DIMS, DELS, GRID )
| 1
......
10157 | ISTAT = NF_GET_VARA_REAL( FID, VID, DIMS, DELS, GRID )
| 2
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
make[1]: *** [modncfio.o] Error 1
make[1]: Leaving directory `/WRF/ioapi-3.2/ioapi'
make: *** [all] Error 2
[root@c31236451db8 ioapi-3.2]#
GROMACS: Use Arm Performance Libraries (Free ArmPL) ?!
WRF: Build failure
Following the steps at https://github.com/Yikun/hpc-arm/blob/main/WRF.md#compiling-and-installing-wrf the compile (step 7) fails with:
time mpif90 -o real_em.o -c -O3 -ftree-vectorize -funroll-loops -march=armv8.2-a -w -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -fopenmp -I../dyn_em -I../dyn_nmm -I/WRF/WRF-4.2/external/esmf_time_f90 -I/WRF/WRF-4.2/main -I/WRF/WRF-4.2/external/io_netcdf -I/WRF/WRF-4.2/external/io_int -I/WRF/WRF-4.2/frame -I/WRF/WRF-4.2/share -I/WRF/WRF-4.2/phys -I/WRF/WRF-4.2/wrftladj -I/WRF/WRF-4.2/chem -I/WRF/WRF-4.2/inc -I/path/to/NETCDF/include real_em.f90
f951: error: unknown value 'armv8.2-a' for -march
0.00user 0.00system 0:00.00elapsed 100%CPU (0avgtext+0avgdata 6824maxresident)k
0inputs+0outputs (0major+742minor)pagefaults 0swaps
make[1]: [real_em.o] Error 1 (ignored)
ranlib libwrflib.a
ranlib: 'libwrflib.a': No such file
I have tried with -march=native but again it fails the same way.
$ gcc -march=native -Q --help=target prints -march= armv8.2-a+crypto+dotprod+fp16fml but once again it fails the same way.
Finally I've removed -march=... altogether from CFLAGS_LOCAL and FCOPTIM and this helped a bit but the build failed later. See the attachment for the full log.
wrf-compile.log.zip
FVCOM: The download link gives 404
http://fvcom.smast.umassd.edu/releases/fvcom-4.3.tar.gz returns error 404.
It might be because I am not logged in.
I've created an account with them but in the confirmation email it says:
Attention please: Our staff will check and verify your account. It will take about 7 business days. Your account will not be valid until that.
Thank you for registering with FVCOM @ MEDML!
So, I won't be able to test FVCOM for now.
FVCOM: Cannot get the source code
FVCOM requires registration to download their source code.
So I am not able to test the steps at https://github.com/Yikun/hpc-arm/blob/main/ROMS.md#compiling-and-installing-roms
I've requested an account with them. Hopefully they will approve it!
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