Issues compiling yambo 5.0 on HPC

[Marzieh]

Dear Daniele,

other files are here.


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

[Marzieh]

Dear Daniele,

I attached the files in my previous message.
I am not sure you get my files or no.
Here I attached other files.


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

[Marzieh]

Dear Daniele,

Yes, Thank you .

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

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

[pyadav]

Dear Developers,

I encountered the following error while installing the updated version of Yambo-5.0.

>>>[Making lib/yambo/interface]<<<
make[1]: Entering directory `/home/pyadav/software/yambo-5.0/lib/yambo/driver/src/interface'
make[1]: *** No targets specified and no makefile found. Stop.
make[1]: Leaving directory `/home/pyadav/software/yambo-5.0/lib/yambo/driver/src/interface'
make: *** [yambo] Error 2

It would be great if someone can help me with this.
Thanks,
Pushpendra

[pyadav]

Dear developers,

After downloading the files "iotk-y1.2.2.tar.gz lapack-3.6.1.tar.gz libxc-2.2.3.tar.gz netcdf-fortran-4.5.2.tar.gz netcdf-fortran-4.5.3.tar.gz scalapack-2.1.0.tar.gz
" I copied them to /yambo-5.0/lib/archive.
After that I'm using the following commands

export fftwdir=~/Software/fftw-3.3.6-pl1/

export mkldir=/home/pyadav/intel2020/compilers_and_libraries_2020/linux/mkl/lib/intel64

./configure CC=icc PFC=mpiifort FC=ifort MPIFC=mpiifort MPIF77=ifort MPICC=mpiicc F77=ifort --enable-dp F90=ifort --with-blas-libs="-Wl,--start-group \
$mkldir/libmkl_intel_lp64.a $mkldir/libmkl_sequential.a $mkldir/libmkl_core.a \
-Wl,--end-group" --with-lapack-libs="-Wl,--start-group $mkldir/libmkl_intel_lp64.a \
$mkldir/libmkl_sequential.a $mkldir/libmkl_core.a -Wl,--end-group" --with-blacs-libs="$mkldir/libmkl_blacs_intelmpi_lp64.a" --with-scalapack-libs="$mkldir/libmkl_scalapack_lp64.a" --with-fft-libs="-L$fftw
dir/lib -lfftw3" --with-fft-path=$fftwdir --with-netcdf-lib=/home/pyadav/netcdf4/lib --with-netcdf-include=/home/pyadav/netcdf4/include/

But I'm getting the following error -

read_upf_v2.f90(722): catastrophic error: Too many errors, exiting
compilation aborted for read_upf_v2.f90 (code 1)
make[1]: *** [read_upf_v2.o] Error 1
make[1]: Leaving directory `/home/pyadav/software/yambo-5.0/lib/qe_pseudo'
make: *** [yambo] Error 2

How can I fix this error?

Thanks,
Pushpendra

[Davide Sangalli]

There was a bug in the compilation of the internal lapack which maybe the source of the error.
In my experience if the lapack compilation fails, then internal iotk are not compiled, and finally qe_pseudo fails because the iotk modules are not found.

You can clone the master or branch 5.0 (which now have the lapack makefile ficed) or simply copy this file
https://github.com/yambo-code/yambo/blo ... ke.inc_lib
it into your source in place of the buggy lib/lapack/make.inc_lib

After that please try to recompile everything.

Best,
D.

[pyadav]

Hi David,

Thank you for your reply.

It looks that, yes, the problem is with the iotk_module

read_upf_v2.f90(18): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [IOTK_MODULE]
USE iotk_module
------------^
read_upf_v2.f90(52): error #6632: Keyword arguments are invalid without an explicit interface.
.
.
.

I followed your suggestion

You can clone the master or branch 5.0 (which now have the lapack makefile ficed) or simply copy this file
https://github.com/yambo-code/yambo/blo ... ke.inc_lib
it into your source in place of the buggy lib/lapack/make.inc_lib

but facing the same error. I also noticed that "libxc build failed".

I would really appreciate any suggestion to fix it up.

Best,
Pushpendra

[Davide Sangalli]

Code: Select all

 I also noticed that "libxc build failed".

Then this is the issue.
Likely the libxc build fails and the iotk are not compiled.
The qe_pseudo compilation fails.
Can you find and report the error message for the libxc compilation ?

[pyadav]

Dear David,

When I tried to configure I got the following message regarding libxc

Code: Select all

checking for libxc... Compatible external LibXC not found/specified. Internal to be compiled.

[ Ic] LibXC     : /home/pyadav/software/yambo-5.0/lib/external/intel/mpiifort/lib/libxcf90.a /home/pyadav/software/yambo-5.0/lib/external/intel/mpiifort/lib/libxc.a
#                   -I/home/pyadav/software/yambo-5.0/lib/external/intel/mpiifort/include

and after make yambo -I'm getting the following message

Code: Select all

>>>[Making libxc]<<<
make[2]: Entering directory `/home/pyadav/software/yambo-5.0/lib/libxc'
( cd ../archive ; if ! test -e libxc-2.2.3.tar.gz ; then \
cp Makefile.loc Makefile ; make libxc-2.2.3.tar.gz ; fi )
gunzip < ../archive/libxc-2.2.3.tar.gz | ../../config/missing --run tar xf -

gzip: stdin: unexpected end of file
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.
make[2]: *** [uncompress-stamp] Error 1
make[2]: Leaving directory `/home/pyadav/software/yambo-5.0/lib/libxc'
make[1]: *** [libxc] Error 2
make[1]: Leaving directory `/home/pyadav/software/yambo-5.0'
libxc build failed

I have kept the 'libxc-2.2.3.tar.gz' file manually into the archive directory but still getting the above error.

best,
Pushpendra

[andrea.ferretti]

Dear Pushpendra,

typically you get errors like

Code: Select all

gzip: stdin: unexpected end of file
tar: This does not look like a tar archive

if the tarball files are corrupted (most likely), or if they have been unzipped during download (this happened to me a few times using OSX).

Did you try to open the tarball archive yourself ?

Code: Select all

tar xvfz libxc-2.2.3.tar.gz

does it work ?