Installing Yambo without internet access on HPC clusters.

Having trouble compiling the Yambo source? Using an unusual architecture? Problems with the "configure" script? Problems in GPU architectures? This is the place to look.

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If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
(4) the version of Yambo (revision number/major release version)
(5) the relevant compiler error message
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Mukesh
Posts: 1
Joined: Sat Apr 02, 2022 2:17 am

Installing Yambo without internet access on HPC clusters.

Post by Mukesh » Sun Apr 03, 2022 4:46 pm

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

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Nicola Spallanzani
Posts: 64
Joined: Thu Nov 21, 2019 10:15 am

Re: Installing Yambo without internet access on HPC clusters.

Post by Nicola Spallanzani » Sun Apr 03, 2022 5:15 pm

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
Nicola Spallanzani, PhD
S3 Centre, Istituto Nanoscienze CNR and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu

Reza_Reza
Posts: 34
Joined: Wed Jan 17, 2024 12:13 pm
Location: France

Re: Installing Yambo without internet access on HPC clusters.

Post by Reza_Reza » Tue May 07, 2024 11:55 am

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
Reza - Postdoc
CNRS

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Daniele Varsano
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Re: Installing Yambo without internet access on HPC clusters.

Post by Daniele Varsano » Thu May 09, 2024 11:22 am

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

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

Reza_Reza
Posts: 34
Joined: Wed Jan 17, 2024 12:13 pm
Location: France

Re: Installing Yambo without internet access on HPC clusters.

Post by Reza_Reza » Thu May 16, 2024 2:01 pm

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
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Reza - Postdoc
CNRS

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Daniele Varsano
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Re: Installing Yambo without internet access on HPC clusters.

Post by Daniele Varsano » Thu May 16, 2024 4:28 pm

Dear Reza,

please post the config.log file.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

Reza_Reza
Posts: 34
Joined: Wed Jan 17, 2024 12:13 pm
Location: France

Re: Installing Yambo without internet access on HPC clusters.

Post by Reza_Reza » Thu May 16, 2024 4:38 pm

Dear Daniele,

I attached the config.log file.

Best,

Reza
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Reza - Postdoc
CNRS

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Daniele Varsano
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Re: Installing Yambo without internet access on HPC clusters.

Post by Daniele Varsano » Thu May 16, 2024 9:42 pm

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
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

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