[Wien] Wien Installation
晨晨
chiniku at qq.com
Mon Jun 22 11:43:13 CEST 2020
Thank you for your reply.
I am installing wien version 19.2 on Linux with gfortran and OpenBlas.
In the “Specify ScaLAPACK settings”, I would like to know how to set the part of “Please specify the target architecture of your ScaLAPACK libraries (e.g. intel64)!:”.
In addition, when the settings are as the following, there are some errors.
Settings:
SCALAPACKROOT:/home/username/scalapack-2.1.0/
SCALAPACK_LIBNAME: libscalapack.a
BLACSROOT: /home/username/BLACS/LIB
BLACS_LIBNAME: blacs_MPI-LINUX-0.a
MKL_TARGET_ARCH: /home/username/scalapack-2.1.0/libscalapack.a
Some errors:
-ftree-vectorize -march=native -ffree-line-length-none -ffpe-summary=none -DFFTW3 -I/home-yg/users/YG_cheny/Soft/fftw-3.3.6-pl2/gcc820/include -fopenmp -L../SRC_lib -L/home-yg/users/YG_cheny/Soft/fftw-3.3.6-pl2/gcc820/lib -lfftw3 /home-yw/soft/packagedir/Openblas-0.39/gcc820/lib/libopenblas.so -L/home-yg/users/YG_cheny/Soft/scalapack-2.1.0//home-yg/users/YG_cheny/Soft/scalapack-2.1.0/libscalapack.a -llibscalapack.a -L/home-yg/users/YG_cheny/Soft/BLACS/LIB//home-yg/users/YG_cheny/Soft/scalapack-2.1.0/libscalapack.a -lblacs_MPI-LINUX-0.a
/usr/bin/ld: cannot find -llibscalapack.a
collect2: error: ld returned 1 exit status
make[1]: *** [hfc_mpi] Error 1
make[1]: Leaving directory `/home-yg/users/YG_cheny/Soft/19.2/SRC_hf'
make: *** [cp] Error 2
------------------ 原始邮件 ------------------
发件人: "Gavin Abo"<gsabo at crimson.ua.edu>;
发送时间: 2020年6月16日(星期二) 上午10:38
收件人: "wien"<wien at zeus.theochem.tuwien.ac.at>;
主题: Re: [Wien] Wien Installation
Those undefined references, such as _intel_fast_memcpy, are defined in an Intel compiler library [1]. When using Intel compilers (ifort/icc/mpiifort), typically mkl is used instead of OpenBLAS as well as the Intel MPI Library [2]. Since you have used the gnu compilers (gfortran/gcc) to compile OpenBLAS, WIEN2k, and your flavor of mpi (whether that be Open-MPI [3], MVAPICH [4], or another one [5]), most likely you need to recompile FFTW3 with your mpi compiler (e.g. [6]) based on gfortran/gcc too.
[1] https://software.intel.com/en-us/forums/intel-c-compiler/topic/815696
[2] https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html
[3] https://www.open-mpi.org/
[4] http://mvapich.cse.ohio-state.edu/
[5] https://en.wikipedia.org/wiki/MPICH#MPICH_derivatives
[6] https://www.open-mpi.org/faq/?category=mpi-apps#general-build
On 6/15/2020 7:36 PM, 晨晨 wrote:
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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