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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?

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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 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 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 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 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 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, 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 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 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 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 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 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 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 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

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