Dalton 2013 on Powerlinux

Problems with Dalton installation? Find answers or ask for help here
Post Reply
afca
Posts: 19
Joined: 11 Nov 2013, 01:23
First name(s): Antonio
Last name(s): Arapiraca
Affiliation: CEFET/MG
Country: Brazil

Dalton 2013 on Powerlinux

Post by afca » 26 Jan 2014, 04:29

Hi,

I'm trying to install Dalton 2013 on IBM Powerlinux 7R2 single node machine running the following configuration:

OS: Red Hat Enterprise Linux Server 6.5
Compilers: IBM Advance Toolchain 6.0 GNU 4.7.3 compilers
MPI: OpenMPI 1.6.5
Maths: Standard Blas and Lapack, ATLAS and Openblas

First of all I compiled 32 and 64 bits versions of OpenMPI following the instructions of http://diracprogram.org/doc/release-12/ ... 4/mpi.html.
The compilations passed in the ompi_info -a | grep 'Fort integer size' test and export the PATH

export PATH=/opt//openmpi64gnu/bin/:$PATH
export LD_LIBRARY_PATH=/opt/openmpi64gnu/bin/lib:$LD_LIBRARY_PATH

In order to compile the code I used the setup command to standard maths case:

./setup --mpi --lapack=/usr/lib64/liblapack.so --blas=/usr/lib64/libblas.so build-openmpi64gnu-standard

and get the following error:

...
[ 18%] Building Fortran object CMakeFiles/dalton.dir/DALTON/abacus/abarspn.F.o
/root/DALTON-2013.1-Source-fnmc/DALTON/abacus/abaqmmm.F: In function ‘qmmmfirst’:
/root/DALTON-2013.1-Source-fnmc/DALTON/abacus/abaqmmm.F:526:0: error: insn does not satisfy its constraints:
(insn 4916 4914 4917 66 (set (reg:DI 10 10)
(reg/f:DI 61 29 [2958])) /root/DALTON-2013.1-Source-fnmc/DALTON/abacus/abaqmmm.F:440 401 {*movdi_internal64}
(nil))
/root/DALTON-2013.1-Source-fnmc/DALTON/abacus/abaqmmm.F:526:0: internal compiler error: in reload_cse_simplify_operands, at postreload.c:403
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://gcc.gnu.org/bugs.html> for instructions.
make[3]: *** [CMakeFiles/dalton.dir/DALTON/abacus/abaqmmm.F.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[2]: *** [CMakeFiles/dalton.dir/all] Error 2
make[1]: *** [CMakeFiles/dalton.x.dir/rule] Error 2
make: *** [dalton.x] Error 2

If I add --int64 in the setup line I get:

Building C object CMakeFiles/dalton.dir/DALTON/dft/fun-becke35.c.o
/root/DALTON-2013.1-Source-fnmc/DALTON/dft/eval-dso.c: In function ‘numdso_collect_info’:
/root/DALTON-2013.1-Source-fnmc/DALTON/dft/eval-dso.c:110:5: warning: passing argument 2 of ‘MPI_Comm_size’ from incompatible pointer type [enabled by default]
In file included from /root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.h:197:0,
from /root/DALTON-2013.1-Source-fnmc/DALTON/dft/eval-dso.c:56:
/opt/openmpi64gnu/include/mpi.h:1113:20: note: expected ‘int *’ but argument is of type ‘integer *’
/root/DALTON-2013.1-Source-fnmc/DALTON/dft/cube-fast.c: In function ‘dft_cr_resp_collect_info’:
/root/DALTON-2013.1-Source-fnmc/DALTON/dft/cube-fast.c:1275:5: warning: passing argument 2 of ‘MPI_Comm_size’ from incompatible pointer type [enabled by default]
In file included from /root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.h:197:0,
from /root/DALTON-2013.1-Source-fnmc/DALTON/dft/integrator.h:13,
from /root/DALTON-2013.1-Source-fnmc/DALTON/dft/cube-fast.c:38:
/opt/openmpi64gnu/include/mpi.h:1113:20: note: expected ‘int *’ but argument is of type ‘integer *’
[ 7%] Building C object CMakeFiles/dalton.dir/DALTON/dft/fun-cam-b3lyp.c.o
[ 7%] [ 7%] Building C object CMakeFiles/dalton.dir/DALTON/dft/fun-example.c.o
...

[ 13%] Building C object CMakeFiles/dalton.dir/DALTON/dft/general.c.o
/root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.c:626:1: error: conflicting types for ‘mpi_sync_data’
In file included from /root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.c:60:0:
/root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.h:216:6: note: previous declaration of ‘mpi_sync_data’ was here
/root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.c: In function ‘dft_wake_slaves’:
/root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.c:646:5: warning: passing argument 2 of ‘MPI_Comm_rank’ from incompatible pointer type [enabled by default]
In file included from /root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.h:197:0,
from /root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.c:60:
/opt/openmpi64gnu/include/mpi.h:1107:20: note: expected ‘int *’ but argument is of type ‘integer *’
/root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.c: In function ‘dft_cslave_’:
/root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.c:693:5: warning: passing argument 2 of ‘MPI_Comm_rank’ from incompatible pointer type [enabled by default]
In file included from /root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.h:197:0,
from /root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.c:60:
/opt/openmpi64gnu/include/mpi.h:1107:20: note: expected ‘int *’ but argument is of type ‘integer *’
/root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.c:694:8: warning: passing argument 2 of ‘MPI_Comm_size’ from incompatible pointer type [enabled by default]
In file included from /root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.h:197:0,
from /root/DALTON-2013.1-Source-fnmc/DALTON/dft/general.c:60:
/opt/openmpi64gnu/include/mpi.h:1113:20: note: expected ‘int *’ but argument is of type ‘integer *’
make[3]: *** [CMakeFiles/dalton.dir/DALTON/dft/general.c.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[2]: *** [CMakeFiles/dalton.dir/all] Error 2
make[1]: *** [CMakeFiles/dalton.x.dir/rule] Error 2
make: *** [dalton.x] Error 2

When I tried the full 32 bits compilation I export the PATH

export PATH=/opt//openmpi32gnu/bin/:$PATH
export LD_LIBRARY_PATH=/opt/openmpi32gnu/bin/lib:$LD_LIBRARY_PATH

and used the following setup line:

./setup --mpi --lapack=/usr/lib/liblapack.so --blas=/usr/lib/libblas.so build-openmpi32gnu-standard

and get the following error:

[ 24%] Building Fortran object CMakeFiles/dalton.dir/DALTON/abacus/abalresc.F.o
[ 24%] Building Fortran object CMakeFiles/dalton.dir/DALTON/abacus/linearlr.F.o
/root/DALTON-2013.1-Source-fnmc/DALTON/abacus/herpar.F:387.72:

& )
1
Error: There is no specific subroutine for the generic 'mpi_file_set_view' at (1)
/root/DALTON-2013.1-Source-fnmc/DALTON/abacus/herpar.F:1403.72:

& ierr )
1
Error: There is no specific subroutine for the generic 'mpi_file_set_view' at (1)
make[3]: *** [CMakeFiles/dalton.dir/DALTON/abacus/herpar.F.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[2]: *** [CMakeFiles/dalton.dir/all] Error 2
make[1]: *** [CMakeFiles/dalton.x.dir/rule] Error 2
make: *** [dalton.x] Error 2

After that I checked my openMPI and the MPI_File_set_view is ok.

Can someone help me?

Regards

Antonio

Reeta Felscia
Posts: 4
Joined: 04 Aug 2014, 17:17
First name(s): Reeta
Last name(s): Felscia
Affiliation: Lady Doak College
Country: India

Re: Dalton 2013 on Powerlinux

Post by Reeta Felscia » 04 Aug 2014, 17:33

Hi,
I'm new to computational physics.I m trying to install Dalton (tar file) using Linux. I don't know how to install it.. plz anyone can help me..?? I'm in need of detailed explanation.. :? :(
Thanks in advance.

Joanna
Posts: 116
Joined: 27 Aug 2013, 16:38
First name(s): Joanna
Last name(s): Kauczor
Affiliation: Helsinki
Country: Finland

Re: Dalton 2013 on Powerlinux

Post by Joanna » 04 Aug 2014, 17:57

Dear Reeta Felscia,

you can find a very detailed explanation here: http://daltonprogram.org/installation/2013/index.html

Reeta Felscia
Posts: 4
Joined: 04 Aug 2014, 17:17
First name(s): Reeta
Last name(s): Felscia
Affiliation: Lady Doak College
Country: India

Re: Dalton 2013 on Powerlinux

Post by Reeta Felscia » 04 Aug 2014, 18:05

Dear Joanna,
Thank you very much for your help :) ... Will contact if i have any further questions...

Reeta Felscia
Posts: 4
Joined: 04 Aug 2014, 17:17
First name(s): Reeta
Last name(s): Felscia
Affiliation: Lady Doak College
Country: India

Re: Dalton 2013 on Powerlinux

Post by Reeta Felscia » 06 Aug 2014, 14:40

Hi,
I'm still struggled with Dalton installation.. I have downloaded the tar file and save it in my desktop... Then what is the next step i have to do..?? Can Dalton supports Boss/ GNU Linux? Can anyone plz help me..?? I don't know anything about Linux Or Dalton... :?

bast
Posts: 1197
Joined: 26 Aug 2013, 13:22
First name(s): Radovan
Last name(s): Bast
Affiliation: none
Country: Germany

Re: Dalton 2013 on Powerlinux

Post by bast » 06 Aug 2014, 14:49

first extract the tarball with "tar xzf".
then with your software manager install CMake, BLAS and LAPACK libraries,
as well as gfortran, gcc, and g++.
then follow http://daltonprogram.org/installation/2013/index.html
i have never used BOSS linux but i am confident that it should be possible.
i also recommend to read a good book about Linux. with this you will
be more efficient. so it's not time lost, but time well invested.
good luck!

Reeta Felscia
Posts: 4
Joined: 04 Aug 2014, 17:17
First name(s): Reeta
Last name(s): Felscia
Affiliation: Lady Doak College
Country: India

Re: Dalton 2013 on Powerlinux

Post by Reeta Felscia » 06 Aug 2014, 14:58

Thank you sir..

abslobodyuk
Posts: 1
Joined: 26 Jul 2015, 05:28
First name(s): Arseny
Last name(s): Slobodyuk
Affiliation: Institute of Chemistry FEBRAS
Country: Russian Federation

Re: Dalton 2013 on Powerlinux

Post by abslobodyuk » 26 Jul 2015, 07:38

afca wrote:
/root/DALTON-2013.1-Source-fnmc/DALTON/abacus/herpar.F:387.72:

& )
1
Error: There is no specific subroutine for the generic 'mpi_file_set_view' at (1)
/root/DALTON-2013.1-Source-fnmc/DALTON/abacus/herpar.F:1403.72:

& ierr )
1
Error: There is no specific subroutine for the generic 'mpi_file_set_view' at (1)
I had the same errors on Debian Linux Wheezy and Jessie when configured to use MPI (./setup --mpi).
Sorry about necroposting, but this thread seems to be the only one about the problem.
My config: MPI: openmpi 1.4.5; compiler: mpif90; GNU BLAS & LAPACK
I've solved it with this patch. IDK exactly how to check if it is really correct.

Code: Select all

--- herpar.F.orig	2015-07-20 21:15:03.000000000 +1000
+++ herpar.F	2015-07-26 12:50:16.000000000 +1000
@@ -301,7 +301,8 @@
 CTROND
 #ifdef VAR_MPI
       integer, parameter             :: dummy_buff = 2
-      integer(kind=MPI_ADDRESS_KIND) :: nelement, displacement
+      integer(kind=MPI_ADDRESS_KIND) :: nelement
+      integer(kind=MPI_OFFSET_KIND)  :: displacement
       character(len=16)              :: shared_dmat_file
       integer                        :: istat(mpi_status_size)
 #endif
@@ -1262,7 +1263,8 @@
 #include "mpif.h"
 #endif
       integer, parameter             :: dummy_buff = 2
-      integer(kind=MPI_ADDRESS_KIND) :: nelement, displacement
+      integer(kind=MPI_ADDRESS_KIND) :: nelement
+      integer(kind=MPI_OFFSET_KIND)  :: displacement
       integer(kind=MPI_ADDRESS_KIND) :: nelement_d, nelement_f
       integer(kind=MPI_ADDRESS_KIND) :: dmat_p, fmat_p
       real(8)                        :: dmat_buff(dummy_buff)

Post Reply

Who is online

Users browsing this forum: No registered users and 2 guests