Installing Yambo without internet access on HPC clusters.

[Mukesh]

Hello all,
I have installed Yambo on our personal group cluster which has internet access. During the installation, I have noticed that installation required internet. But in our institute cluster there is no internet access (Usually HPC do not provide the internet). So my question is:

Is there any to download all the required file and install Yambo without using internet??

If there is instruction guidelines, please feel free to refer that.


Thanks and regards,
Mukesh Singh
Department of Physics
IIT Bombay, India

[Nicola Spallanzani]

Dear Mukesh,
usually HPC clusters have internet connection at least in the login nodes. So you can perform the operations that need the download there and then move to the compute nodes for the compilation. Otherwise you can download all the required libraries in you PC and then copy everything in the cluster. Here the procedure:

# in the login node or in your PC with internet connection
git clone https://github.com/yambo-code/yambo.git
cd yambo
git clone https://github.com/yambo-code/yambo-libraries.git lib/yambo
./configure
make download # this command download all the libs in the directory lib/archive
cd ..
tar zxvf yambo_with_libs.tgz yambo

Now you can copy the file yambo_with_libs.tgz on the cluster and use it for the compilation.

Best regards,
Nicola

[Reza_Reza]

Dear Nicola,

I used this strategy to install Yambo on the IRENE machine (TGCC Joliot Curie), and it worked well. However, the webpage (https://www.yambo-code.eu/wiki/index.ph ... iot_Curie)) needs to be modified because, when using 'make yambo,' it encounters an error:

\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

gzip: stdin: not in gzip format
tar: This does not look like a tar archive
tar: Exiting with failure status due to previous errors
gtar: This does not look like a tar archive
gtar: Exiting with failure status due to previous errors
WARNING: I can't seem to be able to run `tar' with the given
arguments.
You may want to install GNU tar or Free paxutils, or check
the
command line arguments.

I think instead of "make yambo", it must use "make download" and then transfer the file to the IRENE machine.

Best,

Reza

[Daniele Varsano]

Dear Reza,
thanks for posting, we will have a look at it.

Best,
Daniele

[Reza_Reza]

Dear Daniele,

I tried to install yambo on IRENE with open-mp. It works well without problem. However, when i tried to install it with MPI, i cannot compile it.

#load module dependances
module load hdf5/1.8.20
module load blas/mkl/20.0.0
module load netcdf-c/4.6.0
module load netcdf-fortran/4.4.4
module load libxc/5.1.6
module load mpi/openmpi/4


#configure step
./configure FC=ifort F77=ifort CC=icc MPIF77=mpif90 MPICC=mpicc MPIFC=mpif90 --enable-par-linalg --enable-open-mp --with-scalapack-libs=mkl --with-blacs-libs=mkl --with-netcdf-includedir=${NETCDF_INCDIR} --with-netcdf-libs="${NETCDF_LDFLAGS}" --with-netcdff-includedir=${NETCDFFORTRAN_INCDIR} --with-netcdff-libs="${NETCDFFORTRAN_LDFLAGS}" --with-hdf5-libs="${HDF5_LDFLAGS}" --with-hdf5-path=${HDF5_ROOT} --with-hdf5-libdir=${HDF5_LIBDIR} --with-hdf5-includedir=${HDF5_INCDIR} --with-libxc-libs=${LIBXC_LIBDIR} --with-libxc-path=${LIBXC_ROOT} --with-libxc-libdir=${LIBXC_LIBDIR} --with-libxc-includedir=${LIBXC_INCDIR} --enable-hdf5-p2y-support

Best,

Reza

[Daniele Varsano]

Dear Reza,

please post the config.log file.

Best,
Daniele

[Reza_Reza]

Dear Daniele,

I attached the config.log file.

Best,

Reza

[Daniele Varsano]

Dear Reza,
it seems that some mpi libraries are missing in your system:

Code: Select all

mpifort: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory

is it possibile you need to load some modules first? are you able to compile other codes using MPI?
If not, you can try to reinstall openMPI libraries.
Actually it seems yo are trying to use an intel operMPI version with gfortran.

If you have intel compilers you can indicate them in the configure command line as:
./configure FC=ifort CC=icc MPIFC=mpiifort

Best,
Daniele