Compile yambo-3.2.3-rev.11

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

Moderators: Daniele Varsano, andrea.ferretti, andrea marini, Conor Hogan, myrta gruning

Forum rules
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
sdwang
Posts: 212
Joined: Fri Apr 09, 2010 12:30 pm

Compile yambo-3.2.3-rev.11

Post by sdwang » Sat Mar 19, 2011 3:39 am

Dear developers:
I try to complie v-3.2.3,but met some problem. I have two option:
My configure is:
1)../configure --with-iotk=/home/sdwang/espresso-4.1.2/iotk/ --with-p2y=4.0 --with-mpi=/home/sdwang/mpich2/lib/libmpichf90.a,but it appears error: checking for unoptimized flags... -O0 -mtune=native
checking how to get verbose linking output from gfortran... configure: WARNING: compilation failed

checking for Fortran libraries of gfortran...
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... configure: error: in `/home/sdwang/yambo-3.2.3-rev.11':
configure: error: cannot compile a simple Fortran program
See `config.log' for more details. And, the config1.log is in attachment. .In v-3.2.1, this procedure is well.

2).WhenI type :./configure --with-iotk=/home/sdwang/espresso-4.1.2/iotk/ --with-p2y=4.0 --with-mpi=/home/sdwang/mpich2/lib/libmpichf90.a FC=ifort,it works,and the parellel [X] MPI is appear. But in config.log, it can not find the PATH of /home/sdwang/mpich2/bin ,so I cant perform parallel calculation instead of serial one.This correponds to config2.log

How can I solve this problem?(The mpich2 is in my own dir:/home/sdwang, mpich is in /usr/local/, mpich does not work with it, so I install mpich2 in my own dir)

(1) the compiler ( intel 9.0)
(2) the architecture (x86_64-redhat-linux/3.4.4/,HP clusters)
(3)compiling in parallel
(4) the version of Yambo (yambo-3.2.3-rev.11)
You do not have the required permissions to view the files attached to this post.
S. D. Wang
IMU,HOHHOT,CHINA
E-mail: sdwang@imu.edu.cn

User avatar
claudio
Posts: 222
Joined: Tue Mar 31, 2009 11:33 pm
Contact:

Re: Compile yambo-3.2.3-rev.11

Post by claudio » Mon Mar 21, 2011 11:01 am

Dear Shudong Wang

when you compile and execute the code try to include the mpich libraries and the executables in your path, doing, with bash shell:

export PATH="$PATH:/home/sdwang/mpich2/bin/"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/sdwang/mpich2/lib"

and then try again

./configure --with-iotk=/home/sdwang/espresso-4.1.2/iotk/ --with-p2y=4.0 --with-mpi=/home/sdwang/mpich2/lib/libmpichf90.a FC=ifort F77=ifort MPICC=/home/sdwang/mpich2/bin/mpicc

let us know if it works
Claudio
Claudio Attaccalite
Institut Neel, CNRS/UJF ABINEEL group
25 rue des Martyrs BP 166, Bâtiment D
38042 Grenoble cedex 9 France
web site: http://www.attaccalite.com
Freely download scientific books from: http://www.freescience.info

sdwang
Posts: 212
Joined: Fri Apr 09, 2010 12:30 pm

Re: Compile yambo-3.2.3-rev.11

Post by sdwang » Mon Mar 21, 2011 11:33 am

Thank you for your reply.
When I compiled with your guide,it has no error.But when I performed >yambo with parallel version,it has
0 - <NO ERROR MESSAGE> : Could not convert index 1140850688 into a pointer
The index may be an incorrect argument.
Possible sources of this problem are a missing "include 'mpif.h'",
a misspelled MPI object (e.g., MPI_COM_WORLD instead of MPI_COMM_WORLD)
or a misspelled user variable for an MPI object (e.g.,
com instead of comm).
p0_16636: p4_error: : 9039
[0] Aborting program !
[0] Aborting program!

Where is the problem?
S. D. Wang
IMU,HOHHOT,CHINA
E-mail: sdwang@imu.edu.cn

User avatar
andrea marini
Posts: 447
Joined: Mon Mar 16, 2009 4:27 pm
Contact:

Re: Compile yambo-3.2.3-rev.11

Post by andrea marini » Mon Mar 21, 2011 11:36 am

I am a bit lost. First of all can you compile and run a simple parallel source ? Is it your mpich working ? The error you get is really weird and I fear it is not due to Yambo.

Andrea
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)

sdwang
Posts: 212
Joined: Fri Apr 09, 2010 12:30 pm

Re: Compile yambo-3.2.3-rev.11

Post by sdwang » Mon Mar 21, 2011 11:45 am

When I compile v-3.2.1 with same mpich, it woeks well.
S. D. Wang
IMU,HOHHOT,CHINA
E-mail: sdwang@imu.edu.cn

sdwang
Posts: 212
Joined: Fri Apr 09, 2010 12:30 pm

Re: Compile yambo-3.2.3-rev.11

Post by sdwang » Mon Mar 21, 2011 12:21 pm

claudio wrote:Dear Shudong Wang

when you compile and execute the code try to include the mpich libraries and the executables in your path, doing, with bash shell:

export PATH="$PATH:/home/sdwang/mpich2/bin/"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/sdwang/mpich2/lib"

and then try again

./configure --with-iotk=/home/sdwang/espresso-4.1.2/iotk/ --with-p2y=4.0 --with-mpi=/home/sdwang/mpich2/lib/libmpichf90.a FC=ifort F77=ifort MPICC=/home/sdwang/mpich2/bin/mpicc

let us know if it works
Claudio


If I compiled with openmpi, what I should set --with-mpi=????
./configure --with-iotk=/home/sdwang/espresso-4.1.2/iotk/ --with-p2y=4.0 --with-mpi=/home/sdwang/opemmpi/lib/??? FC=ifort F77=ifort MPICC=/home/sdwang/openmpi/bin/mpicc
S. D. Wang
IMU,HOHHOT,CHINA
E-mail: sdwang@imu.edu.cn

User avatar
claudio
Posts: 222
Joined: Tue Mar 31, 2009 11:33 pm
Contact:

Re: Compile yambo-3.2.3-rev.11

Post by claudio » Tue Mar 22, 2011 4:21 pm

Dear Shudong Wang

if you use openmpi just set mpif90 and mpif77 as compilers and then you do not need anything in --with-mpi.
But before testing yambo make sure that your openmpi environment is working properly
try a simple code like this: http://www.lam-mpi.org/tutorials/nd/part1/lab1.f

Claudio
Claudio Attaccalite
Institut Neel, CNRS/UJF ABINEEL group
25 rue des Martyrs BP 166, Bâtiment D
38042 Grenoble cedex 9 France
web site: http://www.attaccalite.com
Freely download scientific books from: http://www.freescience.info

sdwang
Posts: 212
Joined: Fri Apr 09, 2010 12:30 pm

Re: Compile yambo-3.2.3-rev.11

Post by sdwang » Wed May 25, 2011 10:12 am

claudio wrote:Dear Shudong Wang

when you compile and execute the code try to include the mpich libraries and the executables in your path, doing, with bash shell:

export PATH="$PATH:/home/sdwang/mpich2/bin/"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/sdwang/mpich2/lib"

and then try again

./configure --with-iotk=/home/sdwang/espresso-4.1.2/iotk/ --with-p2y=4.0 --with-mpi=/home/sdwang/mpich2/lib/libmpichf90.a FC=ifort F77=ifort MPICC=/home/sdwang/mpich2/bin/mpicc

let us know if it works
Claudio

I recently used your guide to compile v-3.2.3, it seems well. I calculate QP correction with
>yambo -x
>yambo , it's OK
BUt
>yambo -g n -p p ,
>yambo, it appears:
rank 0 in job 3 n36_36764 caused collective abort of all ranks
exit status of rank 0: killed by signal 9

Does this relate my MPICH2? But, the same mpich2 can work well with yambo v-3.2.1.
S. D. Wang
IMU,HOHHOT,CHINA
E-mail: sdwang@imu.edu.cn

User avatar
claudio
Posts: 222
Joined: Tue Mar 31, 2009 11:33 pm
Contact:

Re: Compile yambo-3.2.3-rev.11

Post by claudio » Wed May 25, 2011 10:31 am

Dear Shudong Wang

did you try to run yambo in serial

./yambo -N

does it work?
and
did you try other codes in parallel with your mpich2?

let us know
Claudio
Claudio Attaccalite
Institut Neel, CNRS/UJF ABINEEL group
25 rue des Martyrs BP 166, Bâtiment D
38042 Grenoble cedex 9 France
web site: http://www.attaccalite.com
Freely download scientific books from: http://www.freescience.info

sdwang
Posts: 212
Joined: Fri Apr 09, 2010 12:30 pm

Re: Compile yambo-3.2.3-rev.11

Post by sdwang » Wed May 25, 2011 11:19 am

I use >yambo -N, it has : Segmentation fault.And, I have not test other code with my mpich2.
S. D. Wang
IMU,HOHHOT,CHINA
E-mail: sdwang@imu.edu.cn

Post Reply