yambo-4.2.3 install

[wangqj1]

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

[andrea.ferretti]

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

[wangqj1]

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

[andrea.ferretti]

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

[wangqj1]

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.

[andrea.ferretti]

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

[wangqj1]

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

[wangqj1]

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

[andrea.ferretti]

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

[wangqj1]

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