Installation error

[babak.min]

Hi
I encountered this error when I installed Yambo, please help me

Fatal Error: petsc/finclude/petscsys.h: No such file or directory
compilation terminated.
make[2]: *** [/root/yambo-5.1.1/config/mk/local/rules.mk:9: mod_interfaces.o] Error 1
make[2]: *** Waiting for unfinished jobs....
(/root/yambo-5.1.1/sbin/replacer.sh SET_defaults.tmp_source)
(mv SET_defaults.tmp_source_space SET_defaults.f90)
(echo "gfortran -c -O3 -g -mtune=native -fopenmp -I/root/yambo-5.1.1/include -I/root/yambo-5.1.1/include/headers/common -I/root/yambo-5.1.1/include/headers/parser -I/root/yambo-5.1.1/lib/yambo/driver/include -I/root/yambo-5.1.1/include/driver -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/include/ -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/v4/serial/include -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/v4/serial/include -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/single/include -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/single/include -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/v4/serial/include -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/include -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/include/ -I/root/yambo-5.1.1/lib/yambo/driver/include -I/root/yambo-5.1.1/include/driver SET_defaults.f90" >> /root/yambo-5.1.1/log/"compile_"yambo".log")
(eval gfortran -c -O3 -g -mtune=native -fopenmp -I/root/yambo-5.1.1/include -I/root/yambo-5.1.1/include/headers/common -I/root/yambo-5.1.1/include/headers/parser -I/root/yambo-5.1.1/lib/yambo/driver/include -I/root/yambo-5.1.1/include/driver -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/include/ -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/v4/serial/include -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/v4/serial/include -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/single/include -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/single/include -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/v4/serial/include -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/include -I/root/yambo-5.1.1/lib/external/gfortran/gfortran/include/ -I/root/yambo-5.1.1/lib/yambo/driver/include -I/root/yambo-5.1.1/include/driver SET_defaults.f90 >> /root/yambo-5.1.1/log/"compile_"yambo".log" 2>&1)
(echo "\t[src/modules] SET_defaults" )
[src/modules] SET_defaults
[driver] yambo (checking work to be done)
yambo linking failed. Check log/compile_yambo.log
make[1]: *** [config/mk/global/actions/compile_yambo.mk:42: yambo] Error 1
yambo build failed

[Daniele Varsano]

Dear babak.min,

please sign your post with your name and affiliation, this is a rule of the forum. You can do once for all by filling the signature in your user profile.

In order to spot the compilation problem, you need to attach your config.log file.

Best,
Daniele

[Nicola Spallanzani]

Dear Babak,
it seams that the installation of the PETSc and/or SLEPc failed.
Could you send the config.log file, and the content of the log/ directory?

Best,
Nicola

[babak.min]

Hi dear Nicola,
I have attached some files. The size of the file is large and it is not possible to send all of it
Thanks

[Nicola Spallanzani]

Dear Babak,
in the log directory there should be the files configure_petsc-3.14.6.log and compile_petsc-3.14.6.log.
Could you send them?

Best,
Nicola

[Reza_Reza]

Hello,

I have compiled Yambo on the cluster using ./config (I have attached all the options). While the commands "mpirun p2y" and "mpirun yambo" work during a calculation, the command "yambo -F file.in -J file_job" does not seem to work.

I do not encounter any errors; however, the folder remains empty, indicating that "yambo -F ... -J ..." is not functioning as expected. I have attached the r_setup for mpirun yambo for your review.

In the bin, I have a2y, c2y, p2y, yambo, and ypp.

I attached config.log since it may be useful.

Secondly, I've compiled Yambo with mpi, If I want to compile with OpenMP to perform hybrid calculations, which option and command should be added in ./configure?

Thank you,

[Nicola Spallanzani]

Dear Babak,
for an hybrid installation (mpi+openmp) using intel compilers I suggest you this script:

Code: Select all

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-mpi --enable-open-mp \
    --enable-msgs-comps --enable-time-profile --enable-memory-profile \
    --enable-par-linalg --enable-slepc-linalg \
    --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-extlibs

make -j core
make -j all