Yambo Community Forum

Dear all,
I was compiling the yambo-4.3.2, the information of my server is list below when I configure;
export CC=icc
export FC=ifort
export F77=ifort
export MPIFC=mpif90
export MPICC=mpicc

export FCFLAGS=-O2
export CFLAGS=-O2
export FFLAGS=-O2

export IOTK_ROOT=$HOME/qjwang/soft/qe-6.2/iotk
export NETCDF_ROOT=$HOME/qjwang/soft/netcdf4-needed

./configure \
--prefix=$HOME/qjwang/soft/yambo-4.2.3 \
\
--enable-openmpi=yes --enable-time-profile=yes \
--enable-iotk=yes --enable-netcdf-LFS=yes \
--with-editor=vim --with-p2y-version=6.0 \
\
--with-blas-libs="-L$MKLROOT/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" \
--with-lapack-libs="-L$MKLROOT/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" \
--with-blacs-libs="-L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64" \
--with-scalapack-libs="-L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64" \
\
--with-iotk-libs="$IOTK_ROOT/src/libiotk.a" \
--with-iotk-path=$IOTK_ROOT \
--with-iotk-libdir=$IOTK_ROOT/src \
--with-iotk-includedir=$IOTK_ROOT/src \
\
--with-netcdf-libs="-L$NETCDF_ROOT/lib -lnetcdff -lnetcdf" \
--with-netcdf-path=$NETCDF_ROOT \
--with-netcdf-libdir=$NETCDF_ROOT/lib \
--with-netcdf-includedir=$NETCDF_ROOT/include

configure: WARNING: unrecognized options: --enable-openmpi, --enable-netcdf-LFS
.................................................
.................................................
After I did make all the errors turn up
chmod u+x /home/qjwang/soft/yambo-4.2.3/lib/external/intel/mpif90/v3/lib/*netcdf*.a
make[2]: Leaving directory `/home/qjwang/soft/yambo-4.2.3/lib/netcdff'

>>>[Making slatec]<<<
cp: ?home/qjwang/soft/yambo-4.2.3/lib/slatec/.objects?and lib/slatec/.objects?are the same file
Warning #2216: '=' assumed following macro name "_libslatec" in command-line definition

make[2]: Entering directory `/home/qjwang/soft/yambo-4.2.3/lib/slatec'
/bin/sh: /home/qjwang/qjwang/soft/yambo-4.2.3/sbin/objects_store.sh: No such file or directory
cd /home/qjwang/soft/yambo-4.2.3/lib/slatec; /home/qjwang/soft/yambo-4.2.3/sbin/moduledep.sh avint.o xermsg.o fdump.o j4save.o xercnt.o xerhlt.o xerprn.o xersve.o i1mach.o xgetua.o polfit.o pcoef.o pvalue.o besj0.o besj1.o besk0.o besk1.o csevl.o inits.o r1mach.o besi0.o besk0e.o besi1.o besk1e.o besi0e.o besi1e.o qage.o qag.o qk15.o qk21.o qk31.o qk41.o qk51.o qk61.o qpsrt.o qawo.o qawoe.o qc25f.o qelg.o qcheb.o qwgtf.o qk15w.o qwgtf.o sgtsl.o > /home/qjwang/qjwang/soft/yambo-4.2.3/lib/slatec/make.dep
/bin/sh: /home/qjwang/qjwang/soft/yambo-4.2.3/lib/slatec/make.dep: No such file or directory
make[2]: *** No rule to make target `make.dep', needed by `libslatec.a'. Stop.
make[2]: Leaving directory `/home/qjwang/soft/yambo-4.2.3/lib/slatec'
make[1]: *** [int-libs] Error 2
make[1]: Leaving directory `/home/qjwang/soft/yambo-4.2.3'
yambo build failed

I don't know how to solve it. Every kind help will be appreciated.
Thanks and best regards.
Q. J. Wang
Yunnan normal university

Dear QJ,

this seems to be a problem due to the automatic download of library tarballs.
If one of the tar.gz files is truncated upon download gunzip fails resulting in the error you've got.

First a simple try (which most probably won't work)
* try a make clean_all and do the procedure again (clean_all is important since you need to remove
all the downloaded files)

* time ago I've got a similar error due to a failure of wget. A possible fix is to manually download and copy the
tarball that fails to download to ~yambo/lib/archive
libxc (the one failing in your case) can be taken from here:
http://qe-forge.org/gf/download/frsrele ... 0.3.tar.gz

note that, since wget was failing in my case, I had to download the above file on a separate machine and then
do a scp or alike

* in case the same problem happens also with other libraries, the url of all the libs downloaded by yambo can be
found here:
~yambo/lib/archive/package.list

hope it helps
Andrea

Dear Andrea,
Thank you very much for your kind help, the above problem has been solved according to your advice, however, a new problem comes forth as following:

>>>[Linking ypp_ph]<<<
make[1]: Entering directory `/home/wang/yambo-3.4.2/ypp'
mod_YPP.F ypp_i.F ypp_init.f90:44.43:

use ELPH, ONLY:gsqF_energy_steps
1
Fatal Error: Can't open module file 'elph.mod' for reading at (1): No such file or directory
make[1]: *** [ypp_init.o] Error 1
make[1]: Leaving directory `/home/wang/yambo-3.4.2/ypp'
make: *** [ypp_ph] Error 2

Best regards,
Q. J. Wang
Yunnan normal university

Dear QJ,

I've given a try and the compilation of yambo_ph and ypp_ph works for me (both using intel or gnu environments) for v3.4.2.
Can you provide the details of the machine you are working on ?
While doing that, please send also the config.log file

Andrea

Dear Andrea,
The details of my machine is as following:

Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC)

The config.log file is also attached.

Dear QJ,

finally I was able to reproduce the problem...
Somehow, it seems that compiling yambo before yambo_ph may confuse the dependencies of Makefile.
As a quick and dirty solution, in my case it works to

* clean the distribution (make clean_all)
* configure
* make yambo_ph
* make ypp_ph

In the meantime I'll keep on investigating the issue.

take care
Andrea

Dear Andrea,
I installed the yambo again according to your advice, however, a new error was received when I did "make yambo_ph" :

>>>[Making modules]<<<
make[1]: Entering directory `/home/wang/yambo-3.4.2/src/modules'
mod_pars.F mod_units.F mod_stderr.F mod_parallel.F mod_wrapper.F mod_fields.F mod_collision.F mod_drivers.F mod_FFT.F mod_timing.F mod_logo mod_com.F mod_memory.F mod_R_lattice.F mod_matrix_operate.F mod_D_lattice.F mod_frequency.F mod_vec_operate.F mod_electrons.F mod_wave_func.F mod_interfaces.F mod_interpolate.F mod_X.F mod_functions.F mod_zeros.F mod_pseudo.F mod_BS.F mod_QP.F mod_TDDFT.F mod_ACFDT.F mod_wf_distribute.F mod_IO.F mod_fragments.F mod_ELPH.f90:51.36:

type(levels) :: E_k_p_q
1
Error: Object 'e_k_p_q' at (1) must have the SAVE attribute for default initialization of a component
make[1]: *** [mod_ELPH.o] Error 1
make[1]: Leaving directory `/home/wang/yambo-3.4.2/src/modules'
make: *** [yambo_ph] Error 2

Thank you and best regards
Q. J. Wang
Yunnan normal universiy

Dear Andrea,
I installed the yambo again according to your advice, however, a new error was received when I did "make yambo_ph" :

>>>[Making modules]<<<
make[1]: Entering directory `/home/wang/yambo-3.4.2/src/modules'
mod_pars.F mod_units.F mod_stderr.F mod_parallel.F mod_wrapper.F mod_fields.F mod_collision.F mod_drivers.F mod_FFT.F mod_timing.F mod_logo mod_com.F mod_memory.F mod_R_lattice.F mod_matrix_operate.F mod_D_lattice.F mod_frequency.F mod_vec_operate.F mod_electrons.F mod_wave_func.F mod_interfaces.F mod_interpolate.F mod_X.F mod_functions.F mod_zeros.F mod_pseudo.F mod_BS.F mod_QP.F mod_TDDFT.F mod_ACFDT.F mod_wf_distribute.F mod_IO.F mod_fragments.F mod_ELPH.f90:51.36:

type(levels) :: E_k_p_q
1
Error: Object 'e_k_p_q' at (1) must have the SAVE attribute for default initialization of a component
make[1]: *** [mod_ELPH.o] Error 1
make[1]: Leaving directory `/home/wang/yambo-3.4.2/src/modules'
make: *** [yambo_ph] Error 2

Thank you and best regards
Q. J. Wang
Yunnan normal universiy

Dear QJ,

it compiles properly in my case using gfortran (as you also are doing), so it looks to me as a compiler-dependent problem.
in my case gfortran -v gives
gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04.1)

while in your case you have:
gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC)
which is a rather old compiler (2012)

I would either try to upgrade to a newer compiler version or to switch to yambo-4.0 (which is public as well)

take care
Andrea

Dear Andrea,
I have installed yambo-4.0.2 by your kind help.
Thank you very much.
Best regards


Q. J. Wang


Yunnan normal university