yambo compilation with slepc error

[shobhit21287]

Hello, we are trying to recompile Yambo with the SLEPC solver for BSE since our system is too heavy for full diagonalization. We were running into an issue with the LibXC library (similar issue as viewtopic.php?t=2649), we applied the patch specified therein and then tried to recompile yambo with the following commands:

./configure \
--enable-open-mp \
--enable-msgs-comps \
--enable-time-profile \
--enable-memory-profile \
--with-libxc-path=/storage/software/libxc \
--with-blas-libs="-L/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl" \
--enable-slepc-linalg \
--with-lapack-libs="-L/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl" \
FC=gfortran CC=gcc F77=gfortran CPP="gcc -E"

make -j4 core

config.log attached below. Then we ran into the following issue:

if test -d slepc-3.14.2 ; then \
unset PETSC_DIR; \
unset PETSC_ARCH; \
cd slepc-3.14.2; \
PETSC_DIR=/storage/software/yambo/lib/external/gfortran/mpifort/single \
SLEPC_DIR=/storage/software/yambo/lib/slepc/slepc-3.14.2 \
python3 ./configure --prefix="/storage/software/yambo/lib/external/gfortran/mpifort/single" ; \
fi
Checking environment...
ERROR: You are requesting a prefix install but the arch directory /storage/software/yambo/lib/slepc/slepc-3.14.2/installed-arch-linux2-c-debug-complex already exists and may contain files from previous builds; consider adding option --with-clean
ERROR: See "installed-arch-linux2-c-debug-complex/lib/slepc/conf/configure.log" file for details
make[4]: * [Makefile:34: configure-stamp] Error 1
make[3]: * [config/mk/global/actions/compile_external_libraries.mk:38: slepc] Error 2
make[3]: warning: -j4 forced in submake: resetting jobserver mode.
make[3]: warning: -j4 forced in submake: resetting jobserver mode.
make[2]: warning: -j4 forced in submake: resetting jobserver mode.
make[3]: warning: -j4 forced in submake: resetting jobserver mode.
[lib/qe_pseudo] qe_pseudo (checking work to be done)
make[3]: warning: -j4 forced in submake: resetting jobserver mode.
[lib/slatec] slatec (checking work to be done)
make[3]: warning: -j4 forced in submake: resetting jobserver mode.
[lib/math77] math77 (checking work to be done)
make[3]: warning: -j4 forced in submake: resetting jobserver mode.
[lib/local] local (checking work to be done)
[lib/yambo/driver/src/interface] interface (checking work to be done)
[lib/yambo/driver/src/main] main (checking work to be done)
[lib/yambo/driver/src/options] options (checking work to be done)
make[2]: * No rule to make target 'lib'. Stop.
make[1]: * [config/mk/global/actions/compile_yambo.mk:38: yambo] Error 2
yambo build failed

I am attaching the config log for your reference. Kindly look into it once.

config.log

config.log

[Daniele Varsano]

Dear Shobhit,

I would follow the hint given by the error message:

ERROR: You are requesting a prefix install but the arch directory /storage/software/yambo/lib/slepc/slepc-3.14.2/installed-arch-linux2-c-debug-complex already exists and may contain files from previous builds; consider adding option --with-clean
ERROR: See "installed-arch-linux2-c-debug-complex/lib/slepc/conf/configure.log" file for details

the file /storage/software/yambo/lib/slepc/slepc-3.14.2/installed-arch-linux2-c-debug-complex/lib/slepc/conf/configure.log can also provide information about the failure.

Anyway, as a first attempt I would do:

> make distclean
>./configure #options
> make yambo


Best,
Daniele

[shobhit21287]

Dear Daniele,
I got the followin error after following those steps.

(chmod u+x /storage/home/shobhit21287/yambo/lib/liblocal.a)
(echo "\t[lib/local] liblocal.a (lib)")
[lib/local] liblocal.a (lib)
(touch /storage/home/shobhit21287/yambo/config/stamps_and_lists/liblocal.a.stamp)
MODS=`find . -name '*.mod'`;for modfile in $MODS ; do mv $modfile /storage/home/shobhit21287/yambo/include; done
[lib/yambo/driver/src/interface] interface (checking work to be done)
[lib/yambo/driver/src/main] main (checking work to be done)
[lib/yambo/driver/src/options] options (checking work to be done)
make[2]: *** No rule to make target 'lib'. Stop.
make[1]: *** [config/mk/global/actions/compile_yambo.mk:38: yambo] Error 2
yambo build failed

Best,
Shobhit

[Daniele Varsano]

Dear Shobhit,
I do not know what's happening, you can try the following:
1) delete the directory yambo inside lib

Code: Select all

rm -rf lib/yambo

2) then clone the yambo-libraries repository in the same place:

Code: Select all

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

Best,

Daniele

[shobhit21287]

Dear Daniele,
I removed yambo/lib and then cloned the repository you told me to. After that I again, did make distclean, with the same configuration, as provided in the first post. I have gotten this error.

(chmod u+x /storage/home/shobhit21287/yambo/lib/liblocal.a)
(echo "\t[lib/local] liblocal.a (lib)")
[lib/local] liblocal.a (lib)
(touch /storage/home/shobhit21287/yambo/config/stamps_and_lists/liblocal.a.stamp)
MODS=`find . -name '*.mod'`;for modfile in $MODS ; do mv $modfile /storage/home/shobhit21287/yambo/include; done
[lib/yambo/driver/src/interface] interface (checking work to be done)
[lib/yambo/driver/src/main] main (checking work to be done)
[lib/yambo/driver/src/options] options (checking work to be done)
make[2]: *** No rule to make target 'lib'. Stop.
make[1]: *** [config/mk/global/actions/compile_yambo.mk:38: yambo] Error 2
yambo build failed

Best,
Shobhit

[shobhit21287]

Dear Daniele,
Would there be a step by step guide for Yambo installation so that we can analyse the quasi-particle properties of large and computationally expensive 2D systems? As of now everytime we are done with a step, we usually need to recompile yambo. If there is or if you could maybe guide us for the same, that would be great help.

Best,
Shobhit

[Daniele Varsano]

Dear Shobhit,
it is not clear why you need to recompile Yambo at each step.
Can you report on what kind of error do you experience?

Best,
Daniele