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Installation of OpenMX in IUAC cluster server
Date: 2019/04/29 19:19
Name: Vicky

Dear All,

I am a beginner in this field. I am having account in IUAC (Inter University Accelerator Center) Cluster server and accessing from my laptop using SSH. While installing I am getting the following error

After running command
$make install
Following error come

mpicc -O3 -xHOST -ip -no-prec-div -openmp -I/opt/intel/mkl/include/fftw -I./liberi-091216/source -c openmx.c


Could anyone explain me step by step installation of OpenMX in my account?
メンテ
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Re: Installation of OpenMX in IUAC cluster server ( No.1 )
Date: 2019/04/30 13:49
Name: Naoya Yamaguchi

Hi,

>Following error come
>
>mpicc -O3 -xHOST -ip -no-prec-div -openmp -I/opt/intel/mkl/include/fftw -I./liberi-091216/source -c openmx.c

If it is all of the messages, the installation is normal and please wait for a while. Or if you get more message, please also paste it.

Regards,
Naoya Yamaguchi
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Re: Installation of OpenMX in IUAC cluster server ( No.2 )
Date: 2019/05/01 13:18
Name: Vicky

Following is the error appearing

[vipin_muj@gate source]$ make install
mpicc -O3 -xHOST -ip -no-prec-div -openmp -I/opt/intel/mkl/include/fftw -I./liberi-091216/source -c openmx.c
make: mpicc: Command not found
make: *** [openmx.o] Error 127

メンテ
Re: Installation of OpenMX in IUAC cluster server ( No.3 )
Date: 2019/05/01 13:27
Name: Yung-Ting

It shows that it can't find mpicc. It needs to install MPI for parallelization, such as OpenMPI ( https://www.open-mpi.org/ ).

Best regards,
YT
メンテ
Re: Installation of OpenMX in IUAC cluster server ( No.4 )
Date: 2019/05/21 20:08
Name: Vicky

I have Installed OpenMPI ( https://www.open-mpi.org/ ). But while I am trying to find it by command line "locate" or "whereis", it cannot locate, I don't know what is happening. Could anyone help me in this regard? Following are the o/p when trying to locate

$ locate openmpi
$

OR
$ whereis OpenMPI
OpenMPI:
$

$ locate mpicc
$ whereis mpicc
mpicc:
$



Thank you
メンテ
Re: Installation of OpenMX in IUAC cluster server ( No.5 )
Date: 2019/05/21 21:54
Name: Yung-Ting Lee

(1) Previously, I installed OpenMPI in the Ubuntu 18.04. I paste my memo of OpenMX installation for your reference.

0. sudo apt-get install build-essential

1. Download the package from https://www.open-mpi.org/

2. tar -zxvf openmpi-4.0.1.tar.gz

3. cd openmpi-4.0.1/

4. ./configure

5. make -j 4

generate libmpi.la in ompi folder

6. sudo make install


Also, I installed gfortran, FFTW, LAPACK, and Scalapack packages for OpenMX installation.

Then, I modified paths of CC, FC, and LIB in the makefile. My makefile in my Ubuntu is listed as below for your reference.

------
CC = mpicc -Dscalapack -O3 -Dkcomp -ffast-math -fopenmp -I/usr/local/include -I/home/ytl/MPI/openmpi-4.0.1/ompi/include
FC = mpif90 -Dscalapack -O3 -Dkcomp -ffast-math -fopenmp -I/home/ytl/MPI/openmpi-4.0.1/ompi/include
LIB= -L/usr/local/lib /home/ytl/software/scalapack-2.0.2/libscalapack.a -lfftw3 -L/home/ytl/MPI/openmpi-4.0.1/ompi -lmpi -lmpi_mpifh -L/home/ytl/software/lapack-3.8.0 -llapack -lrefblas -lgfortran
------

(2) In the OpenMX workshop 2018, it also provides a example for installation of OpenMX-3.8: https://t-ozaki.issp.u-tokyo.ac.jp/ISS18/slides-1st/iss20181st_lecture_20180702.pdf .

In addition, one can find the OpenMX hands-on materials (2014) from http://www.openmx-square.org/video_lec/video_lec.html . It gives many examples and tips for OpenMX installation.

Best regards,
YT
メンテ
Re: Installation of OpenMX in IUAC cluster server ( No.6 )
Date: 2019/05/24 19:32
Name: Vicky

Dear OpenMX Users,

I am trying to install OpenMX3.8 on Ubuntu v 19.04; Intel® Xeon(R) Bronze 3106 CPU @ 1.70GHz × 16

Following changes are made in the makefile

CC = mpicc -O3 -fopenmp -I/usr/local/include -I/home/muj/DFT_software/fftw-3.3.8/api
FC = mpif90 -O3 -fopenmp -I/usr/local/include -I/home/muj/DFT_software/fftw-3.3.8/api
LIB= -L/usr/local/lib -mkl=parallel -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lifcore -lmpi -lmpi_f90 -lmpi_f77

Could anyone tell me what does meant by "-L/usr/local/lib" and for what is the purpose of it?

With above changes in the makefile, the following error occurs:

eri-091216/source/sbt/eri_sbt.o ./liberi-091216/source/sbt/log/eri_fsbt.o ./liberi-091216/source/sbt/log/eri_logfsbt.o ./liberi-091216/source/sbt/linear/eri_linfsbt.o -L/usr/local/lib -mkl=parallel -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lifcore -lmpi -lmpi_f90 -lmpi_f77 -lm -o openmx
gcc: error: unrecognized command line option ‘-mkl=parallel’
make: *** [makefile:257: openmx] Error 1

Does it mean MKL is not installed in the system? Could anyone help me in avoiding this error?

Thanks in advance,

メンテ
Re: Installation of OpenMX in IUAC cluster server ( No.7 )
Date: 2019/05/25 12:58
Name: Naoya Yamaguchi

Dear Vicky,

I guess that you might try to install OpenMX on an environment with GCC+OpenMPI without MKL and please try the following:

CC = mpicc -fopenmp -O3 -I/usr/local/include -I/home/muj/DFT_software/fftw-3.3.8/api
FC = mpif90 -fopenmp -O3 -I/usr/local/include -I/home/muj/DFT_software/fftw-3.3.8/api
LIB = -L/usr/local/lib -lfftw3 -llapack -lblas -lmpi -lmpi_mpifh -lgfortran

An option "-L/usr/local/lib" is to specify the directory path (in this example, /usr/local/lib) including libraries such as liblapack.so or libblas.so, and such options are required if a compiler is not able to find them by itself. So, if there is lack of options to specify them, you may fail to install it, and anyway please try the above and tell errors if any.

Regards,
Naoya Yamaguchi
メンテ
Re: Installation of OpenMX in IUAC cluster server ( No.8 )
Date: 2019/05/25 18:15
Name: Vicky

Dear Naoya,

Thank you very much for your reply. I tried to incorporate your suggestions, it show the following error:

$make install
mpicc -O3 -fopenmp -I/usr/local/include -I/home/muj/DFT_software/fftw-3.3.8/api -I./liberi-091216/source openmx.o openmx_common.o Input_std.o Inputtools.o init.o LU_inverse.o ReLU_inverse.o truncation.o readfile.o FT_PAO.o FT_NLP.o FT_ProExpn_VNA.o FT_VNA.o FT_ProductPAO.o Hamiltonian_Cluster.o Hamiltonian_Cluster_Hs.o Overlap_Cluster.o Hamiltonian_Band.o Overlap_Band.o Hamiltonian_Cluster_NC.o Hamiltonian_Band_NC.o Hamiltonian_Cluster_SO.o Get_OneD_HS_Col.o SetPara_DFT.o XC_Ceperly_Alder.o XC_CA_LSDA.o XC_PW92C.o XC_PBE.o XC_EX.o DFT.o ........
........
./liberi-091216/source/eri.o ./liberi-091216/source/eri_ll.o ./liberi-091216/source/eri_sf.o ./liberi-091216/source/eri_interpolate.o ./liberi-091216/source/eri_gtbl.o ./liberi-091216/source/sbt/eri_sbt.o ./liberi-091216/source/sbt/log/eri_fsbt.o ./liberi-091216/source/sbt/log/eri_logfsbt.o ./liberi-091216/source/sbt/linear/eri_linfsbt.o -L/usr/local/lib -lfftw3 -llapack -lblas -lmpi -lmpi_mpifh -lgfortran -lm -o openmx
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [makefile:257: openmx] Error 1


I think it cannot find libraries ass you said like liblapack.so or libblas.so

I also tried to find these libraries. I found the following:

$ whereis liblapack
liblapack:
$ whereis libblas.so
libblas:
$ whereis liblapack.so
liblapack:
$

Please help.

Regards,
Vicky
メンテ
Re: Installation of OpenMX in IUAC cluster server ( No.9 )
Date: 2019/05/26 02:01
Name: Naoya Yamaguchi

Dear Vicky,

I think "whereis" command cannot find the libraries.
Please try the following:
$ sudo apt install liblapack-dev libblas-dev
, and please try to install OpenMX again.

Regards,
Naoya Yamaguchi
メンテ
Re: Installation of OpenMX in IUAC cluster server ( No.10 )
Date: 2019/05/29 17:57
Name: Vicky

Thank you very much for your response.

With the following setting in make file

CC = mpicc -O3 -fopenmp -I/usr/local/bin -I/home/msrc/DFT_software/fftw-3.3.8/api
FC = mpif90 -O3 -fopenmp -I/usr/local/bin -I/home/msrc/DFT_software/fftw-3.3.8/api
LIB = -L/usr/local/lib -lfftw3 -llapack -lblas -lmpi -lmpi_mpifh -lgfortran

Following error is coming:

$ make install
mpicc -O3 -fopenmp -I/usr/local/bin -I/home/msrc/DFT_software/fftw-3.3.8/api -I./liberi-091216/source -c openmx.c
mpicc: error while loading shared libraries: libopen-pal.so.40: cannot open shared object file: No such file or directory
makefile:267: recipe for target 'openmx.o' failed
make: *** [openmx.o] Error 127/home/msrc/DFT_software/openmpi-4.0.1/opal/.libs/libopen-pal.so.40
$

The above said file is there in the following path:

/home/msrc/DFT_software/openmpi-4.0.1/opal/.libs/libopen-pal.so.40

I request you to please help me.

Thanks

Vicky
メンテ
Re: Installation of OpenMX in IUAC cluster server ( No.11 )
Date: 2019/05/29 18:57
Name: Naoya Yamaguchi

Dear Vicky,

Please try the following:

CC = mpicc -O3 -fopenmp -I/usr/local/bin -I/home/msrc/DFT_software/fftw-3.3.8/api
FC = mpif90 -O3 -fopenmp -I/usr/local/bin -I/home/msrc/DFT_software/fftw-3.3.8/api
LIB = -L/usr/local/lib -lfftw3 -llapack -lblas -lmpi -lmpi_mpifh -lgfortran -L/home/msrc/DFT_software/openmpi-4.0.1/opal/.libs

, where I just added an option of "-L/home/msrc/DFT_software/openmpi-4.0.1/opal/.libs" into "LIB".

Regards,
Naoya Yamaguchi
メンテ
Re: Installation of OpenMX in IUAC cluster server ( No.12 )
Date: 2019/05/29 19:07
Name: Vicky

The problem is same. Could you please help me somehow to get rid of this problem.

Regards,
Vicky
メンテ
Re: Installation of OpenMX in IUAC cluster server ( No.13 )
Date: 2019/05/29 19:29
Name: Yung-Ting Lee

Please type "sudo ldconfig" in. Try to compile OpenMX again.

Best regards,
YT
メンテ
Re: Installation of OpenMX in IUAC cluster server ( No.14 )
Date: 2019/05/30 02:54
Name: Naoya Yamaguchi

Dear Vicky,

How about the following?
LIB = -L/usr/local/lib -lfftw3 -llapack -lblas -lmpi -lmpi_mpifh -lgfortran -L/home/msrc/DFT_software/openmpi-4.0.1/lib

And, Dr. Yung-Ting Lee's suggestion seems effective, so please also try it.
If the problem is not solved, there is an option to install OpenMPI by "apt" commands.

Regards,
Naoya Yamaguchi
メンテ

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