Slepc compilation error in yambo 5.1

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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
sitangshu
Posts: 175
Joined: Thu Jan 05, 2017 8:08 am

Slepc compilation error in yambo 5.1

Post by sitangshu » Mon Apr 04, 2022 9:25 am

Dear all,

While installing Yambo 5.1 from git branch with gcc 7.5.0 & python 3, I got this piece of error:
....
....
....
FC installed-arch-linux2-c-debug-complex/obj/pep/f90-mod/slepcpepmod.o
FC installed-arch-linux2-c-debug-complex/obj/nep/f90-mod/slepcnepmod.o
AR installed-arch-linux2-c-debug-complex/lib/libslepc.a
/usr/bin/ar: @installed-arch-linux2-c-debug-complex/lib/libslepc.a.args: No such file or directory
gmake[8]: *** [installed-arch-linux2-c-debug-complex/lib/libslepc.a] Error 1
gmake[7]: *** [slepc_libs] Error 2
*******************************ERROR************************************
Error during compile, check installed-arch-linux2-c-debug-complex/lib/slepc/conf/make.log
Send all contents of ./installed-arch-linux2-c-debug-complex/lib/slepc/conf to slepc-maint@upv.es
************************************************************************
make[6]: *** [all] Error 1
make[5]: *** [all] Error 2
make[4]: *** [package-ready-stamp] Error 2
make[3]: *** [slepc] Error 2


Regards
Sitangshu
Sitangshu Bhattacharya
Indian Institute of Information Technology-Allahabad
India
Web-page: http://profile.iiita.ac.in/sitangshu/
Institute: http://www.iiita.ac.in/

sitangshu
Posts: 175
Joined: Thu Jan 05, 2017 8:08 am

Re: Slepc compilation error in yambo 5.1

Post by sitangshu » Mon Apr 04, 2022 3:56 pm

Here is the SlepC Make.log attached.
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Sitangshu Bhattacharya
Indian Institute of Information Technology-Allahabad
India
Web-page: http://profile.iiita.ac.in/sitangshu/
Institute: http://www.iiita.ac.in/

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Nicola Spallanzani
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Re: Slepc compilation error in yambo 5.1

Post by Nicola Spallanzani » Mon Apr 04, 2022 4:31 pm

Dear Sitangshu,
could you send also the file config/report from the yambo main directory?

Best,
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

sitangshu
Posts: 175
Joined: Thu Jan 05, 2017 8:08 am

Re: Slepc compilation error in yambo 5.1

Post by sitangshu » Mon Apr 04, 2022 4:43 pm

Here it is Nicola.

Thanks
Sitangshu
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Sitangshu Bhattacharya
Indian Institute of Information Technology-Allahabad
India
Web-page: http://profile.iiita.ac.in/sitangshu/
Institute: http://www.iiita.ac.in/

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Nicola Spallanzani
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Re: Slepc compilation error in yambo 5.1

Post by Nicola Spallanzani » Mon Apr 04, 2022 5:06 pm

Sorry I mean the file named "report" inside the directory "config".

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

sitangshu
Posts: 175
Joined: Thu Jan 05, 2017 8:08 am

Re: Slepc compilation error in yambo 5.1

Post by sitangshu » Mon Apr 04, 2022 6:13 pm

Here it is :)

Sitangshu
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Sitangshu Bhattacharya
Indian Institute of Information Technology-Allahabad
India
Web-page: http://profile.iiita.ac.in/sitangshu/
Institute: http://www.iiita.ac.in/

sdwang
Posts: 287
Joined: Fri Apr 09, 2010 12:30 pm

Re: Slepc compilation error in yambo 5.1

Post by sdwang » Tue Apr 05, 2022 8:47 am

Dear developers,
I met the same problem when installing V5.1 as follows:
...
/usr/bin/ar: @installed-arch-linux2-c-debug-complex/lib/libslepc.a.args: No such file or directory
gmake[6]: *** [installed-arch-linux2-c-debug-complex/lib/libslepc.a] Error 1
gmake[5]: *** [slepc_libs] Error 2
*******************************ERROR************************************
Error during compile, check installed-arch-linux2-c-debug-complex/lib/slepc/conf/make.log
Send all contents of ./installed-arch-linux2-c-debug-complex/lib/slepc/conf to slepc-maint@upv.es
************************************************************************
make[4]: *** [all] Error 1
make[3]: *** [all] Error 2
make[2]: *** [package-ready-stamp] Error 2
make[1]: *** [slepc] Error 2

The intel version is 19.1.0.139 I used performing the installation and it is OK for the previous Yambo version.
Thanks!

Shudong
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S. D. Wang
IMU,HOHHOT,CHINA
E-mail: sdwang@imu.edu.cn

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Nicola Spallanzani
Posts: 62
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Re: Slepc compilation error in yambo 5.1

Post by Nicola Spallanzani » Wed Apr 06, 2022 11:00 am

Hi,
I'm able to compile without issues in this way using the intel compilers, intelmpi and mkl:

Code: Select all

git clone https://github.com/yambo-code/yambo.git
cd yambo
git clone https://github.com/yambo-code/yambo-libraries.git lib/yambo

export FC=ifort 
export F77=ifort
export CPP="icc -E -ansi"
export CC=icc 
export FPP="fpp -free -P"
export F90SUFFIX=".f90"
export MPIFC=mpiifort
export MPIF77=mpiifort
export MPICC=mpiicc
export MPICXX=mpiicpc

./configure \
    --enable-open-mp --enable-mpi --enable-slepc-linalg --enable-hdf5-par-io \
    --enable-msgs-comps --enable-time-profile --enable-memory-profile \
    --with-blas-libs="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" \
    --with-lapack-libs="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" \
    --with-scalapack-libs="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64" \
    --with-blacs-libs="-L${MKLROOT}/lib/intel64 -lmkl_blacs_intelmpi_lp64" \
    --with-fft-includedir="${MKLROOT}/include" \
    --with-fft-libs="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" \
    --with-extlibs-path=${HOME}/opt/yambo-ext-libs

make -j4 core 
So, I suggest to you to start from here and, if it works also for you, then add other configure flags and report here in case of issues.
You can also launch

Code: Select all

make -j4 all
if you need the projects executables, otherwise stay with the core ones.
I use the option "-j4" in the make because I noticed some issues in the compilation of the libraries when asking more then 4 parallel elements in the compilation.

Best,
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

sdwang
Posts: 287
Joined: Fri Apr 09, 2010 12:30 pm

Re: Slepc compilation error in yambo 5.1

Post by sdwang » Wed Apr 06, 2022 12:53 pm

Dear Nicola,
I installed the V 5.1 as your suggestion but it failed as:
...
ome/hipeson/yambo/lib/yambo/external//intel/mpiifort/single/include -I/home/hipeson/yambo/lib/yambo/external//intel/mpiifort/v4/parallel/include -I/home/hipeson/yambo/lib/yambo/external//intel/mpiifort/include -I/home/hipeson/intel2020/compilers_and_libraries_2020.0.139/linux/mkl/include -I/home/hipeson/yambo/lib/yambo/driver/include -I/home/hipeson/yambo/include/driver mod_pars.f90 >> /home/hipeson/yambo/log/"compile_"yambo".log" 2>&1)
make[2]: *** [mod_pars.o] Error 1
make[1]: *** [yambo] Error 2
yambo build failed
And in yambo_log the log is:
e -I/home/hipeson/intel2020/compilers_and_libraries_2020.0.139/linux/mkl/include -I/home/hipeson/yambo/lib/yambo/driver/include -I/home/hipeson/yambo/include/driver mod_pars.f90
mod_pars.f90(26): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [NETCDF]
use netcdf
-----^
mod_pars.f90(88): error #6592: This symbol must be a defined parameter, an enumerator, or an argument of an inquiry function that evaluates to a compile-time constant. [NF90_FLOAT]
integer, parameter :: nf90_SP = nf90_float
----------------------------------^
mod_pars.f90(88): error #6404: This name does not have a type, and must have an explicit type. [NF90_FLOAT]
integer, parameter :: nf90_SP = nf90_float
----------------------------------^
compilation aborted for mod_pars.f90 (code 1)

I used intel and mkl both in 2019 and 2021 version.

Thanks!

Shudong
S. D. Wang
IMU,HOHHOT,CHINA
E-mail: sdwang@imu.edu.cn

sitangshu
Posts: 175
Joined: Thu Jan 05, 2017 8:08 am

Re: Slepc compilation error in yambo 5.1

Post by sitangshu » Wed Apr 06, 2022 7:26 pm

Hi Nicola,

1) I incidentally tried to install slepc following this: https://www.youtube.com/watch?v=hqVpaZ-axNk&t=167s
and I could install both petsc and slepc without any problem using openmpi and gcc9. But I did not find any slepc.a lib.

2) I have tried to use the same procedure you mentioned but still getting the libslepc.a error:
/usr/bin/ar: @installed-arch-linux2-c-debug-complex/lib/libslepc.a.args: No such file or directory
gmake[8]: *** [installed-arch-linux2-c-debug-complex/lib/libslepc.a] Error 1
gmake[7]: *** [slepc_libs] Error 2

I have the followings only in our cluster
# FC kind = intel ifort version 18.0.3
# MPI kind= Intel(R) MPI Library 2018 Update 3 for Linux* OS

I am also attaching the report file with intelFC, in case you want to see....

Regards,
Sitangshu
You do not have the required permissions to view the files attached to this post.
Sitangshu Bhattacharya
Indian Institute of Information Technology-Allahabad
India
Web-page: http://profile.iiita.ac.in/sitangshu/
Institute: http://www.iiita.ac.in/

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