Dalton 2013 on Powerlinux
-
- 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
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
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
-
- 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
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.
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.
-
- 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
Dear Reeta Felscia,
you can find a very detailed explanation here: http://daltonprogram.org/installation/2013/index.html
you can find a very detailed explanation here: http://daltonprogram.org/installation/2013/index.html
-
- 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
Dear Joanna,
Thank you very much for your help
... Will contact if i have any further questions...
Thank you very much for your help

-
- 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
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...
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...

-
- Posts: 1210
- Joined: 26 Aug 2013, 13:22
- First name(s): Radovan
- Last name(s): Bast
- Affiliation: none
- Country: Germany
Re: Dalton 2013 on Powerlinux
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!
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!
-
- 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
Thank you sir..
-
- 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
I had the same errors on Debian Linux Wheezy and Jessie when configured to use MPI (./setup --mpi).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)
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)
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