 Re: Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL ( No.1 ) |
- Date: 2024/10/18 00:35
- Name: Naoya Yamaguchi
- Hi,
I assume that this error is a problem that occurs only on your calculator.
How about repeating the installation from the scratch?
You can prepare a new directory and download the tarballs again there.
Regards,
Naoya Yamaguchi
|
| Re: Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL ( No.2 ) |
- Date: 2024/10/18 15:47
- Name: yanyi
- I've tried four times already, but the problem still occurs. Here are my installation steps; maybe you can give me some advice on where I might have gone wrong.
Entered the following on my cluster.
wget "https://www.openmx-square.org/openmx3.9.tar.gz"
tar zxvf openmx3.9.tar.gz
cd openmx3.9/source
wget "https://openmx-square.org/bugfixed/21Oct17/patch3.9.9.tar.gz"
tar zxvf patch3.9.9.tar.gz
vi makefile (edit makefile, the information about makefile as follow)
MKLROOT = /beegfs/software/intel/oneapi/mkl/2021.3.0
CC = mpicc -O3 -x c -flto -ffast-math -fopenmp -I/beegfs/home/by2653/tools/fftw3/include -I${MKLROOT}/include
FC = mpif90 -O3 -ffast-math -fopenmp -I$(MKLROOT)/include
LIB=-L/beegfs/home/by2653/tools/fftw3/lib -lfftw3 \
-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 \
-lmkl_intel_thread -lmkl_core -lmkl_blacs_openmpi_lp64 \
-lmpi_usempif08 -lmpi_usempi_ignore_tkr \
-lmpi_mpifh -liomp5 -lpthread -lm -ldl
make clean
make all （The error mentioned in my previous email occurred at this step. A lot of errors like the following occurred.)
openmx.o:73:1: error: stray ‘\317’ in program
openmx.o:73:1: error: stray ‘\337’ in program
openmx.o:73:1: error: stray ‘\372’ in program
openmx.o:73:1: error: stray ‘\251’ in program
openmx.o:73:1: error: stray ‘\353’ in program
openmx.o:73:1: error: stray ‘\260’ in program
openmx.o:73:1: error: stray ‘\273’ in program
openmx.o:73:1: error: stray ‘\302’ in program
Here is my configuration information：
# gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
...
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)
#gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
...
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)
#mpicc -v
Using built-in specs.
COLLECT_GCC=/usr/bin/gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
...
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)
# mpif90 -v
Using built-in specs.
COLLECT_GCC=/usr/bin/gfortran
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
...
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)
#FFTW3 is newly installed by me.
the local is /beegfs/home/by2653/tools/fftw3
#use the oneapi(it have MKL library)
the locate is /beegfs/software/intel/oneapi/mkl/2021.3.0
#also have openmpi-4.1.6
the locate is /beegfs/home/by2653/tools/openmpi
However, I have still encountered the same error as mentioned above.
Best,
yanyi
 |
| Re: Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL ( No.3 ) |
- Date: 2024/10/18 18:21
- Name: Naoya Yamaguchi
- Dear yanyi,
>gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)
I guess that this error may have induced by too old the GCC.
I found the following: https://github.com/xmake-io/xmake/discussions/3218
You don't seem to have put up all the error messages, but if you are getting the errors in the URL above, I assume your GCC tried to compile with the old C language standard.
At least, GCC 4 is too old to compile the OpenMX code. You should install newer GCC (e.g. GCC 9) in advance.
Regards,
Naoya Yamaguchi
|
| Re: Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL ( No.4 ) |
- Date: 2024/10/19 23:34
- Name: yanyi
- Dear Naoya,
Hi, following your advice, I have installed GCC version 9.4.0, openmpi.
However, during the installation of OpenMX, many warnings and errors occurred (I mentioned this error earlier, and it still exists).
Below you can find the information about these warnings and errors.
-------------------------------------------------------------------------------------
The warning about [inline function ‘Spherical_Bessel’ declared but never defined], you can find more information in this file:
https://github.com/crankiy/openmx-install-error-information/blob/main/warning%20information(1).txt
The warning about [implicit declaration of function ‘XXXX’ [-Wimplicit-function-declaration]], you can find more information in this file:
https://github.com/crankiy/openmx-install-error-information/blob/main/warning%20information(2).txt
The warning about [Type mismatch in argument ‘q’ at (1); passed REAL(8) to COMPLEX(8) [-Wargument-mismatch]], you can find more information in this file:
https://github.com/crankiy/openmx-install-error-information/blob/main/warning%20information(3).txt
More importantly, I still cannot resolve this error【error: stray ‘XXX’ in program，and a lot of garbled characters have appeared.】, you can find more information in this file:
https://github.com/crankiy/openmx-install-error-information/blob/main/error%20information.txt
--------------------------------------------------------------------------
Here is my configuration information：
#gcc version 9.4.0 (GCC). (the local is /beegfs/home/by2653/tools/GCC/gcc9.4.0/bin/gcc)
#which gfortran. (the local is /beegfs/home/by2653/tools/GCC/gcc9.4.0/bin/gfortran)
#which mpicc (the local is /beegfs/home/by2653/tools/OPENMPI/openmpi4.1.6/bin/mpicc)
#which mpif90 (the local is /beegfs/home/by2653/tools/OPENMPI/openmpi4.1.6/bin/mpif90)
#FFTW3 is newly installed by me. (the local is /beegfs/home/by2653/tools/fftw3)
#use the oneapi(it have MKL library) (the locate is /beegfs/software/intel/oneapi/mkl/2021.3.0)
#also installed openmpi-4.1.6 (the locate is /beegfs/home/by2653/tools/OPENMPI/openmpi4.1.6)
--------------------------------------
vi makefile (edit makefile, the information about makefile as follow)
MKLROOT = /beegfs/software/intel/oneapi/mkl/2021.3.0
CC = mpicc -O3 -x c -flto -ffast-math -fopenmp -I/beegfs/home/by2653/tools/fftw3/include -I${MKLROOT}/include
FC = mpif90 -O3 -ffast-math -fopenmp -I$(MKLROOT)/include
LIB=-L/beegfs/home/by2457132/tools/fftw3/lib -lfftw3 -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -liomp5 -lpthread -lm -ldl
--------------------------------------------------------------------------------------------------------------
I still can't find any reason for this. If you could help me resolve these warnings and errors, I would be extremely grateful. Thank you for your assistance.
Best,
yanyi
|
| Re: Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL ( No.5 ) |
- Date: 2024/10/19 23:40
- Name: yanyi
- In my previous email, there was an error in the link. I have corrected some information.
-----------------------
The warning about [inline function ‘Spherical_Bessel’ declared but never defined], you can find more information in this file:
https://github.com/crankiy/openmx-install-error-information/blob/main/warning%20information1.txt
The warning about [implicit declaration of function ‘XXXX’ [-Wimplicit-function-declaration]], you can find more information in this file:
https://github.com/crankiy/openmx-install-error-information/blob/main/warning%20information2.txt
The warning about [Type mismatch in argument ‘q’ at (1); passed REAL(8) to COMPLEX(8) [-Wargument-mismatch]], you can find more information in this file:
https://github.com/crankiy/openmx-install-error-information/blob/main/warning%20information3.txt
More importantly, I still cannot resolve this error【error: stray ‘XXX’ in program，and a lot of garbled characters have appeared.】, you can find more information in this file:
https://github.com/crankiy/openmx-install-error-information/blob/main/error%20information.txt
-------------------------
|
| Re: Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL ( No.6 ) |
- Date: 2024/10/20 03:55
- Name: Naoya Yamaguchi
- Dear yanyi,
Can you show the output for `mpicc -v`?
Regards,
Naoya Yamaguchi
|
| Re: Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL ( No.7 ) |
- Date: 2024/10/20 17:17
- Name: yanyi
- Dear Naoya，
Of course, here are all information about mpicc:
(base) [by2653@mu01 ~]$ mpicc -v
Using built-in specs.
COLLECT_GCC=/beegfs/home/by2653/tools/GCC/gcc9.4.0/bin/gcc
COLLECT_LTO_WRAPPER=/beegfs/home/by2653/tools/GCC/gcc9.4.0/libexec/gcc/x86_64-pc-linux-gnu/9.4.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: ./configure --prefix=/beegfs/home/by2653/tools/GCC/gcc9.4.0 --disable-multilib --enable-threads=posix --disable-checking --enable--long-long --enable-languages=c,c++,fortran --with-gmp=/beegfs/home/by2653/tools/GCC/gmp6.2.1 --with-mpfr=/beegfs/home/by2653/tools/GCC/mpfr4.1.0 --with-mpc=/beegfs/home/by2653/tools/GCC/mpc1.2.1
Thread model: posix
gcc version 9.4.0 (GCC)
Best,
yanyi
|
| Re: Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL ( No.8 ) |
- Date: 2024/10/21 02:17
- Name: Naoya Yamaguchi
- Dear yanyi,
The output shows that `mpicc` correctly uses the new GCC.
Next, please open `openmx.c` with a text editor and check if there are no garbled characters. If there are garbled characters, please unzip the file on another computer to fix the issue.
Regards,
Naoya Yamaguchi
|
| Re: Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL ( No.9 ) |
- Date: 2024/10/21 16:42
- Name: yanyi
- Dear Naoya,
Based on your suggestion, I checked the `openmx.c` file, and there were no garbled characters. Following that, I tried the following two methods:
1.After unzip the `openmx.c` file on another computer, I transferred it to the cluster and then performed the `make` operation.
2.I logged into the cluster from another computer, unzip the files on the cluster to obtain the `openmx.c` file, and then performed the `make` operation.
Unfortunately, both methods resulted in similar errors, and the error still appears in this file:
https://github.com/crankiy/openmx-install-error-information/blob/main/error%20information.txt
This is the `openmx.c` file I extracted; you can also check if it is correct.
https://github.com/crankiy/openmx-install-error-information/blob/main/openmx.c
Best,
yanyi
|
| Re: Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL ( No.10 ) |
- Date: 2024/10/21 22:39
- Name: Naoya Yamaguchi
- Dear yanyi,
>This is the `openmx.c` file I extracted; you can also check if it is correct.
>https://github.com/crankiy/openmx-install-error-information/blob/main/openmx.c
I also tried the compilation with the above `openmx.c`, and it worked well.
I found a similar case in the following thread: https://cmake.org/pipermail/cmake-developers/2016-June/028682.html
The possible cause was discussed on the above thread, and I can guess that `#include` directive picked up the executable file instead of the C header file.
How about checking the directories including the header files?
Regards,
Naoya Yamaguchi
|
| Re: Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL ( No.11 ) |
- Date: 2024/10/28 15:45
- Name: yanyi
- Dear Naoya,
I apologize for the delay in getting back to you, as I have been quite busy recently. Your suggestions have been extremely helpful to me. I realized that the GCC compiler on my computer might not be fully compatible with Intel's MKL, so I decided to switch to using Intel compilers. I have now changed mpicc and mpif90 to mpiicc and mpiifort, respectively. After that, I entered `make all` and `make install` in the terminal, and the following results appeared.
-----------------------------
[by2653@mu01 source]$ make all
.....
.....
.....【Most of the content is not displayed here.】
.....
cp example_mpi_spawn ../work/example_mpi_spawn
gcc gcube2oned.c -lm -o gcube2oned
cp openmx DosMain jx analysis_example esp polB calB Z2FH bandgnu13 bin2txt cube2xsf intensity_map md2axsf tp kSpin BandDispersion ADenBand FermiLoop GridCalc MulPOnly MulPCalc example_mpi_spawn gcube2oned ../work/
[by2653@mu01 source]$ make install
cp openmx ../work/openmx
[by2653@mu01 source]$
---------------
Does this mean that the installation was successful? If it is indeed successful, that would be fantastic! However, many warnings appeared during the process, and I have displayed them below.
-----------------------------------
The warning 1 about [function "XXX XXX" declared implicitly], you can find more information in this file:
https://github.com/crankiy/openmx-install-error-information/blob/main/waring%20information4.txt
The warning 2 is: libmpi.so.12, needed by /beegfs/software/intel/oneapi/mpi/2021.3.0/lib/libmpifort.so, may conflict with libmpi.so.40
---------------
Should I be concerned about these warnings and address them? My main worry is that these warnings might affect my later use of OpenMX.
Thank you very much for your suggestions, and once again, I apologize for the late reply!
Best,
yanyi
|
| Re: Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL ( No.12 ) |
- Date: 2024/10/28 22:01
- Name: Naoya Yamaguchi
- Dear yanyi,
>The warning 1 about [function "XXX XXX" declared implicitly], you can find more information in this file:
>https://github.com/crankiy/openmx-install-error-information/blob/main/waring%20information4.txt
These warning messages do not affect the installation.
>The warning 2 is: libmpi.so.12, needed by /beegfs/software/intel/oneapi/mpi/2021.3.0/lib/libmpifort.so, may conflict with libmpi.so.40
According to this message, there is a shared object (i.e. library) conflict when linking, so environment variables about libraries need to be set to prevent inappropriate ones (`libmpi.so.40`) from being linked.
To avoid errors at running `openmx`, the issue must be resolved for this message.
Regards,
Naoya Yamaguchi
|
| Re: Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL ( No.13 ) |
- Date: 2024/10/29 10:37
- Name: yanyi
- Dear Naoya,
Alright, thank you for your advice and for all the help you've provided.
Best,
yanyi
|
|
Make error OpenMX3.9.9 on Intel(R) Xeon(R) Silver , have gcc , gfortran, intel-MKL