Issues compiling yambo 5.0 on HPC

[DavidPolito93]

Dear developers,

I am trying to compile yambo 5.0 on the cluster of my university.
However I get stuck.

I have loaded libraries:

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module load gnu8/8.3.0
module load intel/libraries/mkl/2019.4.243
module load openmpi3/3.1.4

Then ./configure and make all

However the process is stopped with the following error:

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>>>[Making qe_pseudo]<<<
read_upf_v2.f90:20:12:

         USE iotk_module
            1
Fatal Error: Can't open module file 'iotk_module.mod' for reading at (1): No such file or directory
compilation terminated.
make[1]: *** [read_upf_v2.o] Error 1
make[1]: Leaving directory `/home/dromanin/Programs/yambo-5.0.0/lib/qe_pseudo'
make: *** [yambo] Error 2

I have also tried with the configuration:

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./configure --with-iotk='/home/dromanin/Programs/qe-6.5_Legion/iotk/'

How can I solve this?

Thank you in advance,

Davide Romanin
-----------------------------------------------------
Post-doctoral fellow
Institut des NanoSciences de Paris
Sorbonne Université, CNRS
4 place Jussieu,
75252 PARIS Cedex 05

[andrea.ferretti]

Dear David,

it seems you are compiling without asking for any openmp support or any external libraries, which is an available option, though probably not the optimal one for an HPC environment (of course this makes sense if you want to get started with yambo compilation or just have a look);
in particular, note that you should pass mkl linking flags to yambo's configure. An example of a configure call is the following:

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MKLROOT=/opt/intel/compilers_and_libraries_2020.0.166/linux/mkl

./configure \
  FC=ifort \
  CC=icc \
  --with-fft-libs="-mkl" \
  --with-blas-libs="-L$MKLROOT -lmkl_intel_lp64  -lmkl_sequential -lmkl_core " \
  --with-lapack-libs="-L$MKLROOT -lmkl_intel_lp64  -lmkl_sequential -lmkl_core " \
  --with-scalapack-libs="-L$MKLROOT -lmkl_scalapack_lp64 " \
  --with-blacs-libs="-L$MKLROOT -lmkl_blacs_intelmpi_lp64 " \
  --with-iotk-path="/opt/iotk/y1.2.2-intel" \
  --with-libxc-path="/opt/libxc/2.2.3-intel" \
  --with-hdf5-path="/opt/hdf5/1.12.0-intel" \
  --with-netcdf-path="/opt/netcdf/4.7.4-hdf5-intel" \
  --with-netcdff-path="/opt/netcdff/4.5.2-hdf5-intel" \
  --enable-open-mp \
  --enable-time-profile \
  --enable-memory-profile \
  --enable-msgs-comps

Now,
concerning the compilation problem related to iotk_modules, it could have two sources:
(1) you have tried different compilers (or versions of them) and did not perform a complete clean of the sources (ie compilation is ok but *mod files are mismatched);
(2) if you compiled in parallel, eg using make -j yambo, there can be issues with the dependencies and for some reasons the code reaches files in need of iotk before having compiled iotk itself...

This second case is probably more likely...
In order to sort this out, one just needs to do a make distclean, and the reconfigure and recompile using less parallelism,
either make yambo, or make -j2 yambo (or so)

Andrea

[DavidPolito93]

Dear Andrea,

Thank you for your answer, it was very useful!

I managed to compile yambo and ypp, however I still have problems with p2y. More precisely:

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(mpifort -c -O3 -g -mtune=native   -fopenmp  -I/home/dromanin/Programs/yambo-5.0.0/include -I/home/dromanin/Programs/yambo-5.0.0//include//modules__HDF5_IO_MPI_OPENMP_TIMING -I/home/dromanin/Programs/yambo-5.0.0/include/headers/common -I/home/dromanin/Programs/yambo-5.0.0/include/headers/parser -I/home/dromanin/Programs/yambo-5.0.0/lib/yambo/driver/include/ -I/home/dromanin/Programs/yambo-5.0.0/include/driver -I/home/dromanin/Programs/qe-6.5_Legion/iotk/src -I/home/dromanin/Programs/yambo-5.0.0/lib/external/gfortran/mpifort/v4/serial/include -I/home/dromanin/Programs/yambo-5.0.0/lib/external/gfortran/mpifort/v4/serial/include   -I/home/dromanin/Programs/yambo-5.0.0/lib/external/gfortran/mpifort/v4/serial/include -I/home/dromanin/Programs/yambo-5.0.0/lib/external/gfortran/mpifort/include -I/home/dromanin/Programs/yambo-5.0.0/lib/external/gfortran/mpifort/include/   -I/home/dromanin/Programs/yambo-5.0.0/lib/yambo/driver/include/ -I/home/dromanin/Programs/yambo-5.0.0/include/driver qeh5_module.f90) > /dev/null
qeh5_module.f90:28:6:

   USE h5d
      1
Fatal Error: Can't open module file ‘h5d.mod’ for reading at (1): No such file or directory
compilation terminated.
make[1]: *** [qeh5_module.o] Error 1
make[1]: *** Waiting for unfinished jobs....
qexml.F make[1]: Leaving directory `/home/dromanin/Programs/yambo-5.0.0/interfaces/p2y'
make: *** [p2y] Error 2

Davide
-----------------------------------------------------
Post-doctoral fellow
Institut des NanoSciences de Paris
Sorbonne Université, CNRS
4 place Jussieu,
75252 PARIS Cedex 05

[andrea.ferretti]

Dear Davide,

it seems parallel HDF5 is detected, but without fortran support (not really needed unless your QE is compiled with hdf5).
One option is to switch off the hdf5_p2y support, by configuring with
--disable-hdf5-p2y-support

take care
Andrea

[Marzieh]

Hi Developer,

I compile yambo-5.0.0 on the cluster with these modules and configure:

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module --force purge
module load releases/2020a
module load intel/2020a
module load HDF5/1.10.6-iimpi-2020a
module load netCDF/4.7.4-iimpi-2020a
module load netCDF-Fortran/4.5.2-iimpi-2020a
module load FFTW/3.3.8-gompi-2020a

 
./configure FC="mpiifort" \
--with-blas-libs="-L/opt/sw/arch/easybuild/2020a/software/imkl/2020.1.217-iimpi-2020a/mkl/lib/intel64/ -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" \
--with-lapack-libs="-L/opt/sw/arch/easybuild/2020a/software/imkl/2020.1.217-iimpi-2020a/mkl/lib/intel64/ -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" \
--with-netcdf-libs="-L/opt/sw/arch/easybuild/2020a/software/netCDF/4.7.4-iimpi-2020a/lib64/" \
--with-netcdf-path="/opt/sw/arch/easybuild/2020a/software/netCDF/4.7.4-iimpi-2020a/" \
--with-netcdf-libdir="/opt/sw/arch/easybuild/2020a/software/netCDF/4.7.4-iimpi-2020a/lib64/" \
--with-netcdf-includedir="/opt/sw/arch/easybuild/2020a/software/netCDF/4.7.4-iimpi-2020a/include/" \
--with-netcdff-libs="-L/opt/sw/arch/easybuild/2020a/software/netCDF-Fortran/4.5.2-iimpi-2020a/lib/" \
--with-netcdff-path="/opt/sw/arch/easybuild/2020a/software/netCDF-Fortran/4.5.2-iimpi-2020a/" \
--with-netcdff-libdir="/opt/sw/arch/easybuild/2020a/software/netCDF-Fortran/4.5.2-iimpi-2020a/lib/" \
--with-netcdff-includedir="/opt/sw/arch/easybuild/2020a/software/netCDF-Fortran/4.5.2-iimpi-2020a/include/" \
--with-hdf5-libs="-L/opt/sw/arch/easybuild/2020a/software/HDF5/1.10.6-iimpi-2020a/lib/" \
--with-hdf5-path="/opt/sw/arch/easybuild/2020a/software/HDF5/1.10.6-iimpi-2020a/" \
--with-hdf5-libdir="/opt/sw/arch/easybuild/2020a/software/HDF5/1.10.6-iimpi-2020a/lib/" \
--with-hdf5-includedir="/opt/sw/arch/easybuild/2020a/software/HDF5/1.10.6-iimpi-2020a/include/" \
--with-fft-libs="-L/opt/sw/arch/easybuild/2020a/software/imkl/2020.1.217-iimpi-2020a/mkl/lib/intel64/ -lmkl_core -lmkl_intel_lp64 -lmkl_sequential" \
--with-fft-path="/opt/sw/arch/easybuild/2020a/software/imkl/2020.1.217-iimpi-2020a/mkl/" \
--with-fft-libdir="/opt/sw/arch/easybuild/2020a/software/imkl/2020.1.217-iimpi-2020a/mkl/lib/intel64/" \
--with-fft-includedir="/opt/sw/arch/easybuild/2020a/software/imkl/2020.1.217-iimpi-2020a/mkl/include/fftw/" \
--with-blacs-libs="/opt/sw/arch/easybuild/2020a/software/imkl/2020.1.217-iimpi-2020a/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a" \
--with-scalapack-libs="/opt/sw/arch/easybuild/2020a/software/imkl/2020.1.217-iimpi-2020a/mkl/lib/intel64/libmkl_scalapack_lp64.a" 


make all

when I use
mpirun -np 2 yambo

I have these errors:

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[ERROR] STOP signal received while in[05] Dynamic Dielectric Matrix (PPA)
[ERROR] Reading File ./SAVE//ndb.dipoles; Variable  NOT DEFINED; NetCDF: Unknown file format

 [ERROR] STOP signal received while in[04] Dipoles

 [ERROR] Writing File ./SAVE//ndb.dipoles; Variable  NOT DEFINED; Permission denied

when I run it without mpirun, I mean just
yambo
I do not have any errors.

Could you please tell me how I can solve this Issue?

Best,
Marzieh Ghoohestani, PhD

Institute of Condensed Matter and Nanosciences,
Université Catholique de Louvain,
8 Chemin des étoiles, 1348 Louvain-la-Neuve, Belgium
https://uclouvain.be/en/directories/marzieh.ghoohestani

[andrea.ferretti]

Dear Marzieh,

in order to be helpful we may need a bit more of information.
can you post the yambo input file you are using to run, together with the reports and logs ?

cheers
Andrea

[Marzieh]

Dear Andrea,

I could not attach here. I will send the input files and some output which errors are in by email.


Best,
Marzieh Ghoohestani, PhD

Institute of Condensed Matter and Nanosciences,
Université Catholique de Louvain,
8 Chemin des étoiles, 1348 Louvain-la-Neuve, Belgium
https://uclouvain.be/en/directories/marzieh.ghoohestani

[Daniele Varsano]

Dear Marzieh,
you can upload your files using the "attachments " button after renaming them with an allowed suffix (e.g. .txt).

Best,
Daniele

[Marzieh]

Dear Daniele,

Yes, Thank you .

here is input files and some output which errors are in.

I can not load all files.
I have also this message:

MPI startup(): PMI server not found. Please set I_MPI_PMI_LIBRARY variable if it is not a singleton case.

Best,
Marzieh Ghoohestani, PhD

Institute of Condensed Matter and Nanosciences,
Université Catholique de Louvain,
8 Chemin des étoiles, 1348 Louvain-la-Neuve, Belgium
https://uclouvain.be/en/directories/marzieh.ghoohestani

[Daniele Varsano]

Dear Marzieh,
the files are not attached, please check it and upload them again.

Best,
Daniele