[Wien] Wien Installation

Tue Jun 16 03:36:54 CEST 2020

Thank you for your details.

Now, there is another problem. In order to generate the lapw0_mpi command, when I run “make para” in the SRC_lapw0, a part of the errors is shown as the following and the whole information is attached: 

mpif90 -o ./lapw0_mpi cputim.o modules.o  W2kinit.o fft_modules.o reallocate.o acggac.o ……

ylm.o -ffree-form -O2 -ftree-vectorize -march=native -ffree-line-length-none -ffpe-summary=none  -DFFTW3 -I/home-yw/Soft/fftw-3.3.8/include  -fopenmp -L../SRC_lib  -lfftw3_mpi  -L/home-yw/Soft/fftw-3.3.8/lib -lfftw3  /home-yw/soft/packagedir/Openblas-0.39/gcc820/lib/libopenblas.so

/home-yw/Soft/fftw-3.3.8/lib/libfftw3_mpi.so: undefined reference to `_intel_fast_memcpy'

/home-yw/Soft/fftw-3.3.8/lib/libfftw3_mpi.so: undefined reference to `_intel_fast_memset'

/home-yw/Soft/fftw-3.3.8/lib/libfftw3_mpi.so: undefined reference to `_intel_fast_memmove'

/home-yw/Soft/fftw-3.3.8/lib/libfftw3_mpi.so: undefined reference to `__intel_sse2_strlen'

collect2: error: ld returned 1 exit status

make[1]: *** [lapw0_mpi] Error 1

make[1]: Leaving directory `/home-yg/users/YG_cheny/Soft/19.2/SRC_lapw0'

make: *** [para] Error 2

------------------ 原始邮件 ------------------
发件人: "Gavin Abo"<gsabo at crimson.ua.edu>;
发送时间: 2020年6月8日(星期一) 晚上8:18
收件人: "wien"<wien at zeus.theochem.tuwien.ac.at>;

主题: Re: [Wien] Wien Installation

                               In terms of OpenBLAS-0.3.9 libraries, in           my           OpenBLAS-0.3.9/lib, there are several files as the below:           libopenblas_nehalemp-r0.3.9.a, libopenblas_nehalemp-r0.3.9.so,           libopenblas.so, libopenblas.so.0,           libopenblas.a. Are they as same as yours?
          I have the following, but you have the same       one named "libopenblas.so" that I use.

     username at computername:~/WIEN2k$ ls       ~/OpenBLAS-0.3.9/*.a ~/OpenBLAS-0.3.9/*.so
       /home/username/OpenBLAS-0.3.9/libopenblas.a
       /home/username/OpenBLAS-0.3.9/libopenblas_barcelonap-r0.3.9.a
       /home/username/OpenBLAS-0.3.9/libopenblas_barcelonap-r0.3.9.so
       /home/username/OpenBLAS-0.3.9/libopenblas.so
     In addition, are there         commands such as lapw0_mpi,         lapw1_mpi and lapw1c_mpi generated by installing with         gfortran+OpenBLAS, just         like by installing with ifort?     No, the Intel Parallel Studio XE 2020 Cluster       Edition has the Intel MPI Library [1] that provides intelmpi       making it easy to build the WIEN2k *_mpi files.  For gfortran, it       can be done but it is extra work as one has to install scalapack       [2] and MPI (such as OpenMPI [3]) separately and then include them       in the parallel compiler settings of WIEN2k in order to build the       files.

     [1]  https://software.intel.com/content/www/us/en/develop/tools/parallel-studio-xe.html
     [2] http://www.netlib.org/scalapack/
     [3]       https://www.open-mpi.org/software/ompi/v4.0/

         Then during ./siteconfig_lapw, I choose O           to set libraries “R_LIBS(LAPACK+BLAS)”, then how to set the           “Real libraries”? Would           you like to tell me how set the “Real libraries” parameter so           that could obtain           the result just like your path for R_LIBS as           “-L/home/username/OpenBLAS-0.3.9           -lopenblas -llapack_lapw –lpthread”?

         In my setting, I did a couple of tries and           obtain three kinds of results as below:

         1.                 When I set           the R_LIBS such as           /home/username/OpenBLAS-0.3.9/lib/libopenblas.so (or           libopenblas.so.0, or libopenblas_nehalemp-r0.3.9.so),           then the massage is: /usr/bin/ld: warning: libgfortran.so.3,           needed by           /home-yw/Soft/OpenBLAS-0.3.9/lib/libopenblas.so, may conflict           with           libgfortran.so.5.

         2.                 When I set           the R_LIBS such as /home/username/OpenBLAS-0.3.9/lib           or /home/username/OpenBLAS-0.3.9, then the massage is: file           not recognized: Is           a directory.

         3.                 When I set he           R_LIBS such as  /home/username/OpenBLAS-0.3.9/lib/           libopenblas_nehalemp-r0.3.9.a           (or libopenblas.a), then the error massage is much, including: /home-yw/Soft/OpenBLAS-0.3.9/lib/libopenblas_nehalemp-r0.3.9.a(blas_server.o):           In function `goto_set_num_threads':           blas_server.c:(.text+0x7f3): undefined           reference to `pthread_create'.

         All above relating files were attached.

          Attached is copy of my compile.msg from       SRC_aim that you can compare to yours.
     Below is what I used for a basic WIEN2k 19.2       install that should work for serial and k-point parallel       calculations (but won't work for mpi calculations).  Of note, it       looks like you will need to replace       "/home/username/OpenBLAS-0.3.9" with       "/home-yw/Soft/OpenBLAS-0.3.9/lib" on your system.  Also, you       might notice below that the "-llapack_lapw" of WIEN2k is not       needed since -lopenblas contains it own lapack library.

       username at computername:~/WIEN2k$ ls WIEN2k_INSTALLDATE 
       WIEN2k_INSTALLDATE
       username at computername:~/WIEN2k$ rm WIEN2k_INSTALLDATE
       username at computername:~/WIEN2k$ ./siteconfig
       ...
       continue or stop (c/s) c
       ...
         Selection: LG
       ...
            Press RETURN to continue
       ...
            Your compiler: gfortran
       ...
            Your compiler: gcc
       ...
        Would you like to use LIBXC (that you have installed - usually       not needed)? (y,N): 
       N
       ...
        Do you want to use FFTW (recommended, but for sequential code not       required)? (Y,n): n
       ...
       Selection: R                                                   
            Real libraries=-L/home/username/OpenBLAS-0.3.9 -lopenblas       -lpthread
       ...
        Current settings:
         M   OpenMP switch:           -fopenmp
         O   Compiler options:        -ffree-form -O2 -ftree-vectorize       -march=native -ffree-line-length-none -ffpe-summary=none
         L   Linker Flags:            $(FOPT) -L../SRC_lib
         P   Preprocessor flags       '-DParallel'
         R   R_LIBS (LAPACK+BLAS):    -L/home/username/OpenBLAS-0.3.9       -lopenblas -lpthread
         F   FFTW options:
             FFTW-LIBS:
         X   LIBX options:
             LIBXC-LIBS:

         S   Save and Quit

             To change an item select option.
       Selection: S
       ...
         Shared Memory Architecture? (y/N):y
         Do you know/need a command to bind your jobs to specific nodes?
         (like taskset -c). Enter N / your_specific_command: N
       ...
          (y/N) N
       ...
            Selection: Q
       ...
            Selection: A
       ...
     Compile time errors (if any) were:

       Check file   compile.msg   in the corresponding SRC_* directory       for the 
       compilation log and more info on any compilation problem.
       ...
          Please enter the full path of the perl program: /usr/bin/perl
       ...
        Please enter the full path to your temporary directory: /tmp
       ...
       username at computername:~/WIEN2k$ userconfig
       ...
       username at computername:~/WIEN2k$ gedit ~/.bashrc
       username at computername:~/WIEN2k$ grep LD_LIBRARY ~/.bashrc
       export       LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/OpenBLAS-0.3.9
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