compilation of yambo-3-4-1-rev61

[senersen]

I am trying to compile an older version of yambo, namely yambo-3.4.1-rev61 in parallel, lthough i have a newer version already but does not work with abinit somehow.

I want it to work with abinit-7.10.4. I made a script that got me until some point but i am stuck at >>>[Linking yambo]<<< part. I do not know what to do next. Someone suggested me to use -static-intel but i even do not know how to do that i am that much ignorent of these things.

Here is the script

#!/bin/bash
make clean
module purge
module load Yambo/4.0.2-rev.90-intel-2016a-iimpi
./configure CC="mpiicc" MPICC="mpiicc" FC="mpif90" CPP="cpp" F77="mpiifort" CPPFLAGS="" FCFLAGS="$FCFLAGS" CFLAGS="$CFLAGS" FFLAGS="$FCFLAGS" LDFLAGS="$LDFLAGS -Wl,-rpath=$MKLROOT/lib/intel64" --enable-netcdf-LFS --with-blas="-L/$MKLROOT/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" --with-lapack="-L/$MKLROOT/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" --with-blacs="-L/$MKLROOT/lib/intel64 -lmkl_blacs_intelmpi_lp64" --with-scalapack="-L/$MKLROOT/lib/intel64 -lmkl_scalapack_lp64" --with-fftw="$EBROOTFFTW" --with-netcdf-lib="-lnetcdff -lnetcdf"
LANG=C
LC_ALL=C
make yambo interfaces


This is the list of modules

1) GCCcore/4.9.3 11) zlib/1.2.8-intel-2016a
2) binutils/2.25-GCCcore-4.9.3 12) Szip/2.1-intel-2016a
3) icc/2016.1.150-GCC-4.9.3-2.25 13) HDF5/1.8.16-intel-2016a
4) ifort/2016.1.150-GCC-4.9.3-2.25 14) cURL/7.47.0-intel-2016a
5) iccifort/2016.1.150-GCC-4.9.3-2.25 15) netCDF/4.4.0-intel-2016a
6) impi/5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25 16) netCDF-Fortran/4.4.2-intel-2016a
7) iimpi/8.1.5-GCC-4.9.3-2.25 17) QuantumESPRESSO/5.4.0-intel-2016a
8) imkl/11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25 18) FFTW/3.3.4-intel-2016a-PFFT-20150905
9) intel/2016a 19) ETSF_IO/1.0.4-intel-2016a
10) libxc/3.0.0-intel-2016a 20) Yambo/4.0.2-rev.90-intel-2016a-iimpi

I also attach the log file.

Can you help me compiling this version in parallel?

Thanks in advance

[Daniele Varsano]

Dear Senersen,

3.4.1 is not supported anymore. It is impossible to us to maintain older versions, moreover in the newer versions there are many bug fixes.

3.4.2 and 4.0 should work with abinit-7.x, so please report what kind of problem you encountered and we will try to help you.

Best,
Daniele

[senersen]

Dear Daniele

All right i gave up on yambo 3.4.1. Lets talk about yambo 4.0.4.

I use abinit 7.10.4, i patched it for yambo. i applied a2y command of yambo 4.0.4 which gave no error and created the SAVE folder and filled it with the necessary files. Now i try yambo command and it says
[sener@ganbo60 yambopatchli]$ yambo

[ERROR][NetCDF] NetCDF: Numeric conversion not representable
[sener@ganbo60 yambopatchli]$

By the way yambo is configured with this script;

#!/bin/bash
module load intel/2016a
module load libxc
module load HDF5
module load netCDF
module load netCDF-Fortran
module load QuantumESPRESSO
module load FFTW
module load ETSF_IO
./configure \
CC="mpiicc" MPICC="mpiicc" FC="mpiifort" FCCPP="fpp" F77="mpiifort" \
CPPFLAGS="" FCFLAGS="$FCFLAGS" CFLAGS="$CFLAGS" FFLAGS="$FCFLAGS" \
LDFLAGS="$LDFLAGS -Wl,-rpath=$MKLROOT/lib/intel64" \
--with-blas-libs="-L/$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_blacs_intelmpi_lp64" --with-scalapack-libs="-L/$MKLROOT/lib/intel64 -lmkl_scalapack_lp64" \
--with-iotk-path="$EBROOTQUANTUMESPRESSO/espresso-$EBVERSIONQUANTUMESPRESSO/S3DE/iotk/" \
--with-libxc-path="$EBROOTLIBXC" --with-fft-path="$EBROOTFFTW" \
--with-etsf-io-path="$EBROOTETSF_IO" \
--enable-netcdf-LFS --enable-open-mp --enable-time-profile \
--with-netcdf-libs="-lnetcdff -lnetcdf" --with-hdf5-path="$EBROOTHDF5"
LANG=C
LC_ALL=C
make all

[andrea.ferretti]

Dear Senersen,

can you post the config.log file also for yambo 4.0.4 ?
thanks
Andrea

[senersen]

Dear Andrea

You can find the log file in the attachment.

Thanks in advance,

sener

[senersen]

Do you need /config/report file as well?

sener

[Daniele Varsano]

Dear Sener,
unfortunately in these days I have very limited connection so I cannot have a look to the files you posted in details. Hopefully someone will help you soon. In the meanwhile you can try to recompile the code without linking your compiled netcdf libraries ?(just skip all the netcdf and hdf option). In this way yambo will download automatically and compile the needed netcdf libs, just in case the problem arise for some incompatibility between yambo and the netcdf previously compiled.

Best

Daniele

[andrea.ferretti]

Dear Sener,

the error message comes from the netcdf library itself, and seems to point to some internal conversions from undefined numbers
(p/m inf for floats, integers that are too large for 32 bits, etc)
It seems the problem is quite known in the web for other cases...

Concerning yambo, it would be useful to have a small test case reproducing the problem...
* is your system very large ? (perhaps the problem is related to the system size)
* have you tried compiling yambo without netcdf LFS ?
* in order to better understand where the problem is, could you try to issue
yambo -D (it should stop when trying to read the DB that causes the problem)
and report the output ?
* Last but not least, did you try the e2y interface ? (you should have it compiled)

take care
Andrea

[senersen]

Dear Andrea,

The system i am trying is the one that i used to work on with an old version like 3.3.0. I had no problem with that version like these. Therefore, i assume it should not be too large for yambo to handle it.

I did not try to compile yambo without netcdf LFS, i am going to do that now and let you know what the result is.

I issued yambo -D and got the following output;
[RD./SAVE//ns.db1]------------------------------------------
Bands : 110
K-points : 102
G-vectors [RL space]: 89233
Components [wavefunctions]: 79586
Symmetries [spatial+T-rev]: 12
Spinor components : 1
Spin polarizations : 1
Temperature [ev]: 0.000000
Electrons : 43.00000
WF G-vectors : 89144
Max atoms/species : 4
No. of atom species : 3
Magnetic symmetries : no
- S/N 003197 --------------------------- v.04.00.04 r.0000 -
[RD./SAVE//ns.wf]-------------------------------------------
Fragmentation :yes
Bands in each block : 110
Blocks : 1
- S/N 003197 --------------------------- v.04.00.04 r.0000 -
[RD./SAVE//ns.kb_pp]----------------------------------------
Fragmentation :yes
- S/N 003197 --------------------------- v.04.00.04 r.0000 -


I did not try e2y interface as i believe it works only with the files with an extension .nc which my abinit does not create so missing etsf configuration.