OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2

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OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2

Date: 2024/08/06 09:56
Name: Shunichiro Ito: Dear colleagues,

I am trying to install OpenMX 3.9 on my AlmaLinux 8.7 system (2 sockets, Xeon Gold 6442Y × 2) with Intel oneAPI base toolkit 2024.2 and HPC toolkit.
According to the page (https://www.openmx-square.org/forum/patio.cgi?mode=view&no=3214), I have tried to install with the following makefile.
However, I got the error as follows. Could someone help me?

Thanks a lot in advance.

Best,
Shunichiro

makefile:
```
MKLROOT = /opt/intel/oneapi/mkl/2024.2
CC = mpiicx -O3 -xHOST -qopenmp -fcommon -Wno-error=implicit-function-declaration -Wno-error=implicit-int -I${MKLROOT}/include/fftw
FC = mpiifx -O3 -xHOST -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lifcore -lm -ldl
```

error:
```
mpiicx -O3 -xHOST -qopenmp -fcommon -Wno-error=implicit-function-declaration -Wno-error=implicit-int -I/opt/intel/oneapi/mkl/2024.2/include/fftw -I./elpa-2018.05.001 -c openmx.c
In file included from openmx.c:67:
./openmx_common.h:114:10: fatal error: 'mpi.h' file not found
114 | #include "mpi.h"
| ^~~~~~~
1 error generated.
make: *** [makefile:241: openmx.o] Error 1
```

Page: [1]

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.1 )

Date: 2024/08/06 13:36
Name: Naoya Yamaguchi

Hi,

It appears that the environment variables for MPI are not set right.
Have you completed the settings described on pages 18-19 of https://www.openmx-square.org/Installation_OpenMX_WSL_EN.pdf ?

Regards,
Naoya Yamaguchi

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.2 )

Date: 2024/08/07 15:06
Name: Shunichiro Ito

Dear Naoya,

Thank you very much for your prompt reply.

I have confirmed the settings shown on pages 18-19 of the file.
Here are the version information:

```
$ icx --version
Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0 (2024.2.0.20240602)
Target: x86_64-unknown-linux-gnu
Thread model: posix
InstalledDir: /opt/intel/oneapi/compiler/2024.2/bin/compiler
Configuration file: /opt/intel/oneapi/compiler/2024.2/bin/compiler/../icx.cfg

$ ifort --version
ifort: remark #10448: Intel(R) Fortran Compiler Classic (ifort) is now deprecated and will be discontinued late 2024. Intel recommends that customers transition now to using the LLVM-based Intel(R) Fortran Compiler (ifx) for continued Windows* and Linux* support, new language support, new language features, and optimizations. Use '-diag-disable=10448' to disable this message.
ifort (IFORT) 2021.13.0 20240602
Copyright (C) 1985-2024 Intel Corporation. All rights reserved.

$ ifx --version
ifx (IFX) 2024.2.0 20240602
Copyright (C) 1985-2024 Intel Corporation. All rights reserved.

$ mpirun --version
Intel(R) MPI Library for Linux* OS, Version 2021.13 Build 20240515 (id: df72937)
Copyright 2003-2024, Intel Corporation.
```

However, I have still encountered the same error as mentioned above.

Best,
Shunichiro

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.3 )

Date: 2024/08/07 17:39
Name: Naoya Yamaguchi

Dear Ito-san,

Can you paste the output of executing a command `env | grep "${I_MPI_ROOT}"/include` ?

Regards,
Naoya Yamaguchi

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.4 )

Date: 2024/08/08 10:23
Name: Shunichiro Ito

Dear Naoya,

Sure! Here is the output of the command.

```
$ env | grep "${I_MPI_ROOT}"/include
CPATH=/opt/intel/oneapi/tbb/2021.13/env/../include:/opt/intel/oneapi/mpi/2021.13/include:/opt/intel/oneapi/mkl/2024.2/include:/opt/intel/oneapi/ippcp/2021.12/include:/opt/intel/oneapi/ipp/2021.12/include:/opt/intel/oneapi/dpl/2022.6/include:/opt/intel/oneapi/dpcpp-ct/2024.2/include:/opt/intel/oneapi/dnnl/2024.2/include:/opt/intel/oneapi/dev-utilities/2024.2/include:/opt/intel/oneapi/dal/2024.5/include/dal:/opt/intel/oneapi/ccl/2021.13/include
```

Best,
Shunichiro

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.5 )

Date: 2024/08/08 16:10
Name: Naoya Yamaguchi

Dear Ito-san,

Thank you. The MPI-related environment variables seem to be set appropriately.
Next, can you also show the output for `ls "${I_MPI_ROOT}"/include`?

Regards,
Naoya Yamaguchi

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.6 )

Date: 2024/08/08 16:50
Name: Shunichiro Ito

Dear Naoya,

Thank you very much.
Here is the output.

```
$ ls "${I_MPI_ROOT}"/include
mpi mpicxx.h mpif.h mpi.h mpiof.h mpio.h
```

Best,
Shunichiro

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.7 )

Date: 2024/08/08 18:23
Name: Naoya Yamaguchi

Dear Ito-san,

From the output results, I think that oneAPI has been installed successfully and there is no file corruption.

The other possible cause is that you might be using an old session, that is, a shell that does not reflect your settings.

How about trying to install OpenMX in a new session, or at least in a session that returned the result of the last command output, or after a reboot?

Regards,
Naoya Yamaguchi

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.8 )

Date: 2024/08/08 19:30
Name: Shunichiro Ito

Dear Naoya,

I have rebooted the system and tried to install OpenMX again, but I still got the same error...
Could you have other options?

I really appreciate all your help.

Best,
Shunichiro

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.9 )

Date: 2024/08/08 23:02
Name: Naoya Yamaguchi

Dear Ito-san,

I have tried an installation of AlmaLinux 8 on WSL. I used "AlmaLinux 8 WSL" available from Microsoft Store, and the installation was successful.

I used DNF to install oneAPI as explained in https://www.intel.com/content/www/us/en/developer/tools/oneapi/hpc-toolkit-download.html?operatingsystem=linux&linux-install-type=dnf , and if you use WSL, how about resetting the AlmaLinux OS?

Regards,
Naoya Yamaguchi

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.10 )

Date: 2024/08/10 17:42
Name: Hiroyuki Kawai

Dear Ito-san,

I previously tried to compile/build OpenMX 3.9.9 with Intel oneAPI 2024 as the compiler as you did, but failed (although the error displayed at that time was different from yours).
Please try to compile/build OpenMX 3.9.9 using Intel oneAPI 2023 instead of Intel oneAPI 2024.

Regards,
Hiroyuki Kawai

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.11 )

Date: 2024/08/11 18:42
Name: Naoya Yamaguchi

Dear Ito-san,

I overlooked that you seems to use a AlmaLinux OS-based workstation, not WSL. Can you show the output for `icx -E -v /dev/null`?

Regards,
Naoya Yamaguchi

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.12 )

Date: 2024/08/12 15:14
Name: Shunichiro Ito

Dear Hiroyuki,

Thank you very much for your reply.
I do not have Intel oneAPI 2023. Could I download it from somewhere?

Best,
Shunichiro

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.13 )

Date: 2024/08/12 15:15
Name: Shunichiro Ito

Dear Naoya,

Yes, I do work with a workstation based on AlmaLinux.
Here is the output:

```
$ icx -E -v /dev/null
Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0 (2024.2.0.20240602)
Target: x86_64-unknown-linux-gnu
Thread model: posix
InstalledDir: /opt/intel/oneapi/compiler/2024.2/bin/compiler
Configuration file: /opt/intel/oneapi/compiler/2024.2/bin/compiler/../icx.cfg
Found candidate GCC installation: /usr/lib/gcc/x86_64-redhat-linux/8
Selected GCC installation: /usr/lib/gcc/x86_64-redhat-linux/8
Candidate multilib: .;@m64
Candidate multilib: 32;@m32
Selected multilib: .;@m64
(in-process)
"/opt/intel/oneapi/compiler/2024.2/bin/compiler/clang" -cc1 -triple x86_64-unknown-linux-gnu -E -disable-free -clear-ast-before-backend -disable-llvm-verifier -discard-value-names -main-file-name null -mrelocation-model static -fveclib=SVML -faltmathlib=SVMLAltMathLibrary -mframe-pointer=none -fapprox-func -funsafe-math-optimizations -fno-signed-zeros -mreassociate -freciprocal-math -fdenormal-fp-math=preserve-sign,preserve-sign -ffp-contract=fast -fno-rounding-math -complex-range=promoted -mconstructor-aliases -funwind-tables=2 -target-cpu x86-64 -mllvm -x86-enable-unaligned-vector-move=true -tune-cpu generic -debugger-tuning=gdb -fdebug-compilation-dir=/home/sookuu/Calculation/ito_s -v -fcoverage-compilation-dir=/home/sookuu/Calculation/ito_s -fclang-abi-compat=17 -resource-dir /opt/intel/oneapi/compiler/2024.2/lib/clang/19 -I/opt/intel/oneapi/tbb/2021.13/env/../include -I/opt/intel/oneapi/mpi/2021.13/include -I/opt/intel/oneapi/mkl/2024.2/include -I/opt/intel/oneapi/ippcp/2021.12/include -I/opt/intel/oneapi/ipp/2021.12/include -I/opt/intel/oneapi/dpl/2022.6/include -I/opt/intel/oneapi/dpcpp-ct/2024.2/include -I/opt/intel/oneapi/dnnl/2024.2/include -I/opt/intel/oneapi/dev-utilities/2024.2/include -I/opt/intel/oneapi/dal/2024.5/include/dal -I/opt/intel/oneapi/ccl/2021.13/include -internal-isystem /opt/intel/oneapi/compiler/2024.2/bin/compiler/../../opt/compiler/include -internal-isystem /opt/intel/oneapi/compiler/2024.2/lib/clang/19/include -internal-isystem /usr/local/include -internal-isystem /usr/lib/gcc/x86_64-redhat-linux/8/../../../../x86_64-redhat-linux/include -internal-externc-isystem /include -internal-externc-isystem /usr/include -O2 -ferror-limit 19 -fheinous-gnu-extensions -fgnuc-version=4.2.1 -fskip-odr-check-in-gmf -fcolor-diagnostics -vectorize-loops -vectorize-slp -mllvm -disable-hir-generate-mkl-call -mllvm -loopopt=1 -floopopt-pipeline=light -mllvm -intel-abi-compatible=true -D__GCC_HAVE_DWARF2_CFI_ASM=1 -fintel-compatibility -fintel-libirc-allowed -fintel-libimf-allowed -o - -x c /dev/null
clang -cc1 version 19.0.0git based upon LLVM 19.0.0git default target x86_64-unknown-linux-gnu
ignoring nonexistent directory "/usr/lib/gcc/x86_64-redhat-linux/8/../../../../x86_64-redhat-linux/include"
ignoring nonexistent directory "/include"
#include "..." search starts here:
#include <...> search starts here:
/opt/intel/oneapi/tbb/2021.13/env/../include
/opt/intel/oneapi/mpi/2021.13/include
/opt/intel/oneapi/mkl/2024.2/include
/opt/intel/oneapi/ippcp/2021.12/include
/opt/intel/oneapi/ipp/2021.12/include
/opt/intel/oneapi/dpl/2022.6/include
/opt/intel/oneapi/dpcpp-ct/2024.2/include
/opt/intel/oneapi/dnnl/2024.2/include
/opt/intel/oneapi/dev-utilities/2024.2/include
/opt/intel/oneapi/dal/2024.5/include/dal
/opt/intel/oneapi/ccl/2021.13/include
/opt/intel/oneapi/compiler/2024.2/bin/compiler/../../opt/compiler/include
/opt/intel/oneapi/compiler/2024.2/lib/clang/19/include
/usr/local/include
/usr/include
End of search list.
# 1 "/dev/null"
# 1 "<built-in>" 1
# 1 "<built-in>" 3
# 391 "<built-in>" 3
# 1 "<command line>" 1
# 1 "<built-in>" 2
# 1 "/dev/null" 2
```

Best,
Shunichiro

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.14 )

Date: 2024/08/12 16:28
Name: Naoya Yamaguchi

Dear Ito-san,

Thanks for the output results. From this information, we can see that the compiler will properly look for the directory containing the header files.
Therefore, I think there is some problem with the system, especially with regard to permissions.

Can you show the output for the following commands?

1. `which mpiicx`
2. `stat /opt/intel/oneapi/mpi/2021.13`
3. `stat /opt/intel/oneapi/mpi/2021.13/include`

Regards,
Naoya Yamaguchi

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.15 )

Date: 2024/08/15 07:56
Name: Shunichiro Ito

Dear Naoya,

Thank you very much. Here are the outputs:

```
$ which mpiicx
/usr/bin/which: no mpiicx in (/home/sookuu/.pyenv/plugins/pyenv-virtualenv/shims:/home/sookuu/.pyenv/shims:/home/sookuu/.pyenv/bin:/usr/local/qe-7.3.1/bin/:/home/sookuu/.local/bin:/home/sookuu/bin:/usr/local/molpro/molpro_2024.1/bin:/usr/share/Modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/gaussian16c01/gauopen:/usr/local/gaussian16c01/g16/bsd:/usr/local/gaussian16c01/g16:/opt/pbs/bin)
```

```
$ stat /opt/intel/oneapi/mpi/2021.13/
File: /opt/intel/oneapi/mpi/2021.13/
Size: 135 Blocks: 0 IO Block: 4096 directory
Device: 824h/2084d Inode: 1649232405 Links: 10
Access: (0755/drwxr-xr-x) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 2024-08-02 13:32:36.542571906 +0900
Modify: 2024-08-02 13:32:41.577505534 +0900
Change: 2024-08-02 13:32:41.577505534 +0900
Birth: 2024-08-02 13:32:36.542571906 +0900
```

```
$ stat /opt/intel/oneapi/mpi/2021.13/include/
File: /opt/intel/oneapi/mpi/2021.13/include/
Size: 89 Blocks: 0 IO Block: 4096 directory
Device: 824h/2084d Inode: 20360607 Links: 3
Access: (0755/drwxr-xr-x) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 2024-08-02 13:32:39.186537052 +0900
Modify: 2024-08-02 13:32:41.577505534 +0900
Change: 2024-08-02 13:32:41.577505534 +0900
Birth: 2024-08-02 13:32:39.186537052 +0900
```

Best,
Shunichiro

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.16 )

Date: 2024/08/15 13:04
Name: Naoya Yamaguchi

Dear Ito-san,

Are the preferences different from when the error first occurred?

It is reported that `mpiicx` is missing from the output of `which mpiicx`.

If the preferences are different, could you restore the earlier preferences and check again?

Regards,
Naoya Yamaguchi

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.17 )

Date: 2024/08/15 13:47
Name: Shunichiro Ito

Dear Naoya,

I am sorry for my mistake. Here are the correct outputs:

```
$ which mpiicx
/opt/intel/oneapi/mpi/2021.13/bin/mpiicx
```

```
$ stat /opt/intel/oneapi/mpi/2021.13/
File: /opt/intel/oneapi/mpi/2021.13/
Size: 135 Blocks: 0 IO Block: 4096 directory
Device: 824h/2084d Inode: 1649232405 Links: 10
Access: (0755/drwxr-xr-x) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 2024-08-02 13:32:36.542571906 +0900
Modify: 2024-08-02 13:32:41.577505534 +0900
Change: 2024-08-02 13:32:41.577505534 +0900
Birth: 2024-08-02 13:32:36.542571906 +0900
```

```
$ stat /opt/intel/oneapi/mpi/2021.13/include/
File: /opt/intel/oneapi/mpi/2021.13/include/
Size: 89 Blocks: 0 IO Block: 4096 directory
Device: 824h/2084d Inode: 20360607 Links: 3
Access: (0755/drwxr-xr-x) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 2024-08-02 13:32:39.186537052 +0900
Modify: 2024-08-02 13:32:41.577505534 +0900
Change: 2024-08-02 13:32:41.577505534 +0900
Birth: 2024-08-02 13:32:39.186537052 +0900
```

Best,
Shunichiro

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.18 )

Date: 2024/08/16 00:40
Name: Naoya Yamaguchi

Dear Ito-san,

Thank you for your report. Permissions to the directories appear to be fine.

In that environment, please run `make install` again to see if it does not work, and then execute `stat /opt/intel/oneapi/mpi/2021.13/include/mpi.h`.
Can you show the output?

Regards,
Naoya Yamaguchi

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.19 )

Date: 2024/08/16 15:30
Name: Shunichiro Ito

Dear Naoya,

I deeply appreciate your support.
I did `make install` but got the same error again. I didn't find any difference in the output of `stat /opt/intel/oneapi/mpi/2021.13/include/mpi.h` before and after `make install`.
Here are the results:

```
$ stat /opt/intel/oneapi/mpi/2021.13/include/mpi.h
File: /opt/intel/oneapi/mpi/2021.13/include/mpi.h
Size: 243094 Blocks: 480 IO Block: 4096 regular file
Device: 824h/2084d Inode: 20360608 Links: 1
Access: (0644/-rw-r--r--) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 1970-01-01 09:00:00.000000000 +0900
Modify: 2024-05-15 23:29:58.000000000 +0900
Change: 2024-08-02 13:32:41.576505547 +0900
Birth: 2024-08-02 13:32:39.186537052 +0900

$ sudo make install
[sudo] password for xxxxxx:
mpiicx -O3 -xHOST -qopenmp -fcommon -Wno-error=implicit-function-declaration -Wno-error=implicit-int -I/opt/intel/oneapi/mkl/2024.2/include/fftw -I./elpa-2018.05.001 -c openmx.c
In file included from openmx.c:67:
./openmx_common.h:114:10: fatal error: 'mpi.h' file not found
114 | #include "mpi.h"
| ^~~~~~~
1 error generated.
make: *** [makefile:228: openmx.o] Error 1
sookuu@sookuu [/usr/local/openmx3.9/source]

$ stat /opt/intel/oneapi/mpi/2021.13/include/mpi.h
File: /opt/intel/oneapi/mpi/2021.13/include/mpi.h
Size: 243094 Blocks: 480 IO Block: 4096 regular file
Device: 824h/2084d Inode: 20360608 Links: 1
Access: (0644/-rw-r--r--) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 1970-01-01 09:00:00.000000000 +0900
Modify: 2024-05-15 23:29:58.000000000 +0900
Change: 2024-08-02 13:32:41.576505547 +0900
Birth: 2024-08-02 13:32:39.186537052 +0900
```

Best,
Shunichiro

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.20 )

Date: 2024/08/17 03:02
Name: Naoya Yamaguchi

Dear Ito-san,

The cause is your operation, there is nothing wrong with your system or libraries. You are trying to install under `/usr/local`.
`/usr/local` is often used as the installation destination when a user with administrative privileges installs on a system. It is especially used when installing from source, rather than using a package management tool such as `dnf`.

`/usr/local` is owned by `root`, so you run `sudo make install`. However, the necessary preferences are not done for `root`, and this issue occurred. This is supported by the lack of access history to `mpi.h`.

The solution is one of the following.

1. Install `openmx` under your home directory

2. Install `openmx` under `/usr/local` after switching the user to `root`

Solution 1 is the same as demonstrated in the installation manual.

In Solution 2, you should use `su` or login as `root`, instead of `sudo`.

My recommendation is Solution 1, and I think Solution 2 is possible if you are familiar with doing source installations against the system.

Regards,
Naoya Yamaguchi

Re: OpenMX 3.9 Installation on an AlmaLinux 8.7 system with Intel oneAPI 2024.2 ( No.21 )

Date: 2024/08/19 09:49
Name: Shunichiro Ito

Dear Naoya,

Solution 1 works well! It's my easy mistake...
Thank you very much for your continuous support.

Best,
Shunichiro

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