Compiling with parallel built

Having trouble compiling the Yambo source? Using an unusual architecture? Problems with the "configure" script? This is the place to look.

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If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
(4) the version of Yambo (revision number/major release version)
(5) the relevant compiler error message

Compiling with parallel built

Postby amirmehdi89 » Sun Apr 08, 2018 10:26 pm

Dear Yambo users and developers,

I am a new user to Yambo 4.1.4 and I have followed most of the tutorials provided. When I compiled Yambo on a supercomputer the first time, I had loaded prerequisite modules that I thought it would need to compile properly, and it worked perfectly fine until I realized it was a serial built. Thereafter, I've been trying to build it parallel with the following configure:
./configure --with-mpi-libs

but every time I look at my r_setup file it says Serial Build at the top of the file. The command that I use (following the tutorials) for running in parallel is:

mpirun -np 2 yambo -F (and the rest)

but it seems that it does the same calculation in two identical files. Long story short, my inquires are as follows:

1. Is this version of Yambo that I have (4.1.4) parallelizable?
2. If so, I'd appreciate a step by step for building it.
3. Am I using the right command for running the parallel?

Thank you very much everyone for helping me out.


Amir M. Mofrad
University of Missouri-Columbia
Chemical Engineering Department
Amir M. Mofrad
University of Missouri-Columbia
Chemical Engineering Department
amirmehdi89
 
Posts: 12
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Re: Compiling with parallel built

Postby Daniele Varsano » Mon Apr 09, 2018 7:52 am

Dear Amir,

you can see in the file ./config/report if the source has been compiled in parallel mode. You should find something like:
Code: Select all
# - PARALLEL SUPPORT -
#
# [X] MPI


If this is not the case it means that something went wrong in the compilation with MPI and you can have a look at your config.log (e.g. different version of serial and parallel compiler etc.).
Please consider that:
Code: Select all
./configure --with-mpi-libs
needs you specify the mpi libraries you want to use.
In general, it is enough to indicate the MPI wrapper.

You can upload here your config.log and will have a look.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
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Re: Compiling with parallel built

Postby amirmehdi89 » Mon Apr 09, 2018 3:02 pm

Thank you very much for your reply. Attached please find the config.log file.

I had openmpi, netcdf, and fftw modules loaded when I did ./configure and in the report, it is similar to what you said it should look like. However, I still can't run it parallel and I don't know if I'm not using a right command to do so or something is wrong in the compilation process. Thank you
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Amir M. Mofrad
University of Missouri-Columbia
Chemical Engineering Department
amirmehdi89
 
Posts: 12
Joined: Wed Apr 04, 2018 12:15 am

Re: Compiling with parallel built

Postby Daniele Varsano » Mon Apr 09, 2018 3:34 pm

Dear Amir,
please sign your post with your affiliation. You can do once for by filling the signature in your profile.

I can't see anything wrong with your config file. Can you post also your ./config/report file?
Are you sure that you have a serial build also after this configure?
Please check if you mpirun wrapper is ok, or if you have other like mpiexec.

Do other codes run in parallel in your machine?

As a final consideration I strongly suggest you to switch to a more recent versione of the code (4.2).

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
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Re: Compiling with parallel built

Postby amirmehdi89 » Mon Apr 09, 2018 5:16 pm

I just got the newer version and I will let you know. Thank you for your help Daniele.

P.S. Yes, other codes work fine in parallel.
Amir M. Mofrad
University of Missouri-Columbia
Chemical Engineering Department
amirmehdi89
 
Posts: 12
Joined: Wed Apr 04, 2018 12:15 am

Re: Compiling with parallel built

Postby amirmehdi89 » Wed Apr 11, 2018 10:43 pm

Regarding this post, I just wanted to let you know I was able to build Yambo in MPI built. Thank you for your help Daniele.
Amir M. Mofrad
University of Missouri-Columbia
Chemical Engineering Department
amirmehdi89
 
Posts: 12
Joined: Wed Apr 04, 2018 12:15 am

Re: Compiling with parallel built

Postby Daniele Varsano » Thu Apr 12, 2018 9:07 am

Great!!
Enjoy yambo in its full capability,

Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
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Re: Compiling with parallel built

Postby burkzdemir » Mon Feb 04, 2019 1:04 pm

Dear Yambo Developers,

I compiled Yambo with parallel. However, when I run with multiple processors it seems to be running Yambo multiple times with single processor. What could be the problem?
Burak Ozdemir
Post-doc, UNAM,
Bilkent University, Ankara, Turkey
burkzdemir
 
Posts: 34
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Re: Compiling with parallel built

Postby Daniele Varsano » Mon Feb 04, 2019 1:25 pm

Dear Burak,
the problem could be related to your MPI libraries or your job launch script.
Impossible to say more with such poor information.
The ./config/setup file can help in spotting the problem.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
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Daniele Varsano
 
Posts: 2027
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Re: Compiling with parallel built

Postby burkzdemir » Mon Feb 04, 2019 3:02 pm

Following is my setup file.


#========================================================
# Yambo 4.2.4 r.14795 h.84793e9c3 setup
#========================================================
#
# Main setup
#
package_string = Yambo 4.2.4 r.14795 h.84793e9c3
cpu = x86_64
os = linux
keep_objs = yes
make = make
ar = ar
arflags = -ru
cc = gcc
cflags = -g -O2 -D_C_US -D_FORTRAN_US
cpp = gcc -E
cppflags = -P
fpp = gfortran -E -P -cpp
fc = gfortran
fc_kind = gfortran
fcflags = -g -O3 -mtune=native
fcuflags = -g -O0 -mtune=native
f90suffix = .f90
f77 = gfortran
fflags = -g -O3 -mtune=native
fuflags = -g -O0 -mtune=native
package_bugreport = yambo@yambo-code.org
shell = /bin/sh
#
# Paths
#
prefix = /truba/home/bozdemir/yambo-4.2.4
exec_prefix = /truba/home/bozdemir/yambo-4.2.4/bin
libs_prefix = /truba/home/bozdemir/yambo-4.2.4/lib/external
srcdir = /truba/home/bozdemir/yambo-4.2.4
prefix = /truba/home/bozdemir/yambo-4.2.4
libdir = /truba/home/bozdemir/yambo-4.2.4/lib
includedir = /truba/home/bozdemir/yambo-4.2.4/include
sysinclude = /truba/home/bozdemir/yambo-4.2.4/include/system
lblas = -L/truba/home/bozdemir/yambo-4.2.4/lib/external/gfortran/gfortran/lib -lblas
llapack = -L/truba/home/bozdemir/yambo-4.2.4/lib/external/gfortran/gfortran/lib -llapack
lblacs =
lscalapack =
lmpi =
impi =
mpiidir =
mpildir =
lopenmp =
lnetcdf = -L/truba/home/bozdemir/yambo-4.2.4/lib/external/gfortran/gfortran/v3/lib -lnetcdf -lm -lcurl
inetcdf = -I/truba/home/bozdemir/yambo-4.2.4/lib/external/gfortran/gfortran/v3/include
lnetcdff = -L/truba/home/bozdemir/yambo-4.2.4/lib/external/gfortran/gfortran/v3/lib -lnetcdff
inetcdff = -I/truba/home/bozdemir/yambo-4.2.4/lib/external/gfortran/gfortran/v3/include
netcdf_opt = --disable-netcdf-4
netcdf_ver = v3
netcdf_flag = -DgFortran
lhdf5 =
ihdf5 =
hdf5_opt =
llibxc = -L/truba/home/bozdemir/yambo-4.2.4/lib/external/gfortran/gfortran/lib -lxcf90 -lxc
ilibxc = -I/truba/home/bozdemir/yambo-4.2.4/lib/external/gfortran/gfortran/include
lfft = -L/truba/home/bozdemir/yambo-4.2.4/lib/external/gfortran/gfortran/lib -lfftw3
ifft = -I/truba/home/bozdemir/yambo-4.2.4/lib/external/gfortran/gfortran/include/
liotk = -L/truba/home/bozdemir/yambo-4.2.4/lib/external/gfortran/gfortran/lib -liotk
iiotk = -I/truba/home/bozdemir/yambo-4.2.4/lib/external/gfortran/gfortran/include/
letsf =
ietsf =
#
# VPATH
#
VPATH = $$topdir
#
Burak Ozdemir
Post-doc, UNAM,
Bilkent University, Ankara, Turkey
burkzdemir
 
Posts: 34
Joined: Tue Sep 09, 2014 7:57 pm

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