internal library (iotk) compilation problem (make all failed)

[muhammadhasan]

Hi,

I am trying to install Yambo 5.3.0 (Git version) on HPC cluster, and I'm facing problems during the internal library (iotk) compilation step. Would you please help me to solve the problem? Here are the details(config.log also attached):
Compiler info:
Compiler: GCC 11.2.0 with OpenMPI 4.0.6
FC: mpif90
CC: mpicc
Architecture:
System: x86_64 architecture
OS: Linux (RedHat-based)
Serial or Parallel build?
Problem occurs both in serial and parallel builds (tried make -j8 and make)
Yambo version
Yambo 5.3.0 (from Git, branch: master)

This is my job file:

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#!/bin/bash
#SBATCH --nodes=1           # Total # of nodes 
#SBATCH --ntasks=14          # Total # of MPI tasks
#SBATCH --time=4-00:00:00   # Total run time limit (hh:mm:ss)
#SBATCH -o yambo_install.out  # Name of stdout output file
#SBATCH -e yambo_install.err  # Name of stderr error file
#SBATCH -p shared           # Queue (partition) name

# Set unlimited memory lock
ulimit -l unlimited

# Load required modules
module purge
module load gcc/11.2.0 openmpi/4.0.6 fftw/3.3.8 openblas/0.3.17 hdf5/1.10.7 netcdf-c/4.7.4 netcdf-fortran/4.5.3

# Set environment variables for Fortran precompiler
export FC=gfortran
export MPIFC=mpif90
export FCFLAGS="-cpp"

make clean
make distclean

./configure --enable-open-mp CC=mpicc FC=mpif90 F77=mpif90 FCFLAGS="-fopenmp" CFLAGS="-fopenmp" FPP="cpp -P"

# Check if configure succeeded
if [ $? -ne 0 ]; then
  echo "Configure failed. Check yambo_install.err for details."
  exit 1
fi

# Compile Yambo
make all

# Check if make succeeded
if [ $? -ne 0 ]; then
  echo "Make failed. Check yambo_install.err for details."
  exit 1
fi

Here is the error file's info:

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The following modules were not unloaded:
  (Use "module --force purge" to unload all):

  1) xalt/2.10.45
sed: -e expression #1, char 14: unknown option to `s'
cp: cannot stat 'iotk-y1.2.2/src/*.a': No such file or directory
chmod: cannot access '/anvil/projects/x-mch240098/software_installation/git_yambo/yambo-5.3.0-git/lib/external/unknown/mpif90/lib/*iotk*.a': No such file or directory
cp: cannot stat 'iotk-y1.2.2/src/*.x': No such file or directory
objects.mk:8: *** missing separator (did you mean TAB instead of 8 spaces?).  Stop.
grep: /anvil/projects/x-mch240098/software_installation/git_yambo/yambo-5.3.0-git/log/compile_qe_pseudo.log: No such file or directory
make[2]: *** [Makefile:58: int-libs] Error 1
make[1]: *** [config/mk/global/actions/compile_yambo.mk:40: yambo] Error 2
make: *** [Makefile:54: all] Error 1

Part of the outputfile:

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\t[iotk-y1.2.2] configuration
\t[iotk-y1.2.2] loclib_only compilation
\t[iotk-y1.2.2] iotk.x compilation
\t[iotk-y1.2.2] installation
\t[hdf5-1.12.2] configuration
\t[hdf5-1.12.2]  compilation
\t[hdf5-1.12.2] installation
\t[netcdf-c-4.9.0] configuration
\t[netcdf-c-4.9.0]  compilation
\t[netcdf-c-4.9.0] installation
\t[netcdf-fortran-4.6.0] configuration
\t[netcdf-fortran-4.6.0]  compilation
\t[netcdf-fortran-4.6.0] installation
\t[libxc-5.2.3] download libxc-5.2.3.tar.gz
\t[libxc-5.2.3] autoconf
\t[libxc-5.2.3] configuration
\t[libxc-5.2.3]  compilation
\t[libxc-5.2.3] installation
\t[lapack-3.12.0] configuration
\t[lapack-3.12.0] compilation
\t[lapack-3.12.0] installation
\t[fftw-3.3.10] download fftw-3.3.10.tar.gz
\t[fftw-3.3.10] configuration
\t[fftw-3.3.10]  compilation
\t[fftw-3.3.10] installation
\t[devicexlib-0.8.5] download devicexlib-0.8.5.tar.gz
\t[devicexlib-0.8.5] configuration
\t[devicexlib-0.8.5] all compilation
\t[devicexlib-0.8.5] installation
\t[lib/qe_pseudo] qe_pseudo (setup)
qe_pseudo build failed
yambo build failed
Make failed. Check yambo_install.err for details.

Best Regards
Md Jahid Hasan
PhD student, Mechanical Engineering
University of Maine

[Nicola Spallanzani]

Dear Hasan,
please try again with this configure line without the other variable definitions:

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make distclean
./configure --enable-open-mp CC=mpicc FC=mpif90 F77=mpif90

If it is still failing please send the content of the directory "log/" and the two files config/report and config/setup.

Best regards,
Nicola

[muhammadhasan]

Hi Dr Nicola,

Thank you so much for your reply.
When I use configure as shown below, there are no files inside the log folder and config/setup, config/report are not generated.

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module load gcc/11.2.0 openmpi/4.0.6 fftw/3.3.8 openblas/0.3.17 hdf5/1.10.7 netcdf-c/4.7.4 netcdf-fortran/4.5.3

make clean
make distclean
./configure --enable-open-mp CC=mpicc FC=mpif90 F77=mpif90 

make all

It shows the following error message on the time.

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configure: error: Found FC precompiler problems in processing FC source.

However, If I add the tag FPP="cpp -P", then it generates the config/setup, config/report files.

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./configure --enable-open-mp CC=mpicc FC=mpif90 F77=mpif90 FPP="cpp -P"

Also, it throws error message as follows:

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config/mk/global/no_configure_help.mk:27: *** Stopping here.  Stop.
config/mk/global/no_configure_help.mk:27: *** Stopping here.  Stop.
sed: -e expression #1, char 14: unknown option to `s'
cp: cannot stat 'iotk-y1.2.2/src/*.a': No such file or directory
chmod: cannot access '/anvil/projects/x-mch240098/software_installation/yambo-5.3.0-git/lib/external/unknown/mpifort/lib/*iotk*.a': No such file or directory
cp: cannot stat 'iotk-y1.2.2/src/*.x': No such file or directory
objects.mk:8: *** missing separator (did you mean TAB instead of 8 spaces?).  Stop.
grep: /anvil/projects/x-mch240098/software_installation/yambo-5.3.0-git/log/compile_qe_pseudo.log: No such file or directory
make[2]: *** [Makefile:58: int-libs] Error 1
make[1]: *** [config/mk/global/actions/compile_yambo.mk:40: yambo] Error 2
make: *** [Makefile:54: all] Error 1

I am sharing the files config/setup, config/report and log folder (with tag FPP="cpp -P") in the attachment if it helps you.

Thank you!

Best Regards
Md Jahid Hasan
PhD student, Mechanical Engineering
University of Maine

[Nicola Spallanzani]

Dear Hasan,
sorry, my fault. The right configure line is this one:

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make distclean
./configure --enable-open-mp CC=gcc FC=gfortran F77=gfortran MPICC=mpicc MPIFC=mpif90 MPIF77=mpif90 

The problem was that the configure was not able to identify the "kind" of the fortran compiler, in this case gfortran.
After the right recognition of the fortran compiler, the yambo configure will automatically set the variable FPP="gfortran -E -P -cpp". If not, you can define if manually.

Best regards,
Nicola

[muhammadhasan]

Hi Dr. Nicola,

Thank you so much. it works and successfully installed on the HPC.

Thank you!

Best Regards
Md Jahid Hasan
PhD student, Mechanical Engineering
University of Maine