Compile yambo-3.2.3-rev.11
Moderators: Davide Sangalli, andrea.ferretti, myrta gruning, andrea marini, Daniele Varsano, Conor Hogan, Nicola Spallanzani
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
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
-
- Posts: 287
- Joined: Fri Apr 09, 2010 12:30 pm
Compile yambo-3.2.3-rev.11
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)
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.
- claudio
- Posts: 456
- Joined: Tue Mar 31, 2009 11:33 pm
- Location: Marseille
- Contact:
Re: Compile yambo-3.2.3-rev.11
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
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
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com
-
- Posts: 287
- Joined: Fri Apr 09, 2010 12:30 pm
Re: Compile yambo-3.2.3-rev.11
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?
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?
- andrea marini
- Posts: 325
- Joined: Mon Mar 16, 2009 4:27 pm
- Contact:
Re: Compile yambo-3.2.3-rev.11
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
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
Istituto di Struttura della Materia, CNR, (Italy)
-
- Posts: 287
- Joined: Fri Apr 09, 2010 12:30 pm
Re: Compile yambo-3.2.3-rev.11
When I compile v-3.2.1 with same mpich, it woeks well.
-
- Posts: 287
- Joined: Fri Apr 09, 2010 12:30 pm
Re: Compile yambo-3.2.3-rev.11
If I compiled with openmpi, what I should set --with-mpi=????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
./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
- claudio
- Posts: 456
- Joined: Tue Mar 31, 2009 11:33 pm
- Location: Marseille
- Contact:
Re: Compile yambo-3.2.3-rev.11
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
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
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com
-
- Posts: 287
- Joined: Fri Apr 09, 2010 12:30 pm
Re: Compile yambo-3.2.3-rev.11
I recently used your guide to compile v-3.2.3, it seems well. I calculate QP correction withclaudio 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
>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.
- claudio
- Posts: 456
- Joined: Tue Mar 31, 2009 11:33 pm
- Location: Marseille
- Contact:
Re: Compile yambo-3.2.3-rev.11
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
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
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com
-
- Posts: 287
- Joined: Fri Apr 09, 2010 12:30 pm
Re: Compile yambo-3.2.3-rev.11
I use >yambo -N, it has : Segmentation fault.And, I have not test other code with my mpich2.