Search found 249 matches

by bast
10 Mar 2014, 23:03
Forum: Running Dalton
Topic: Dalton Exits Without Any Errors
Replies: 6
Views: 7530

Re: Dalton Exits Without Any Errors

hi Jean, about the RAM, not sure it is the problem here but it could be since Dalton allocates more than the work array. there are static allocations from the binary, the work array, and dynamic allocations on top of that. perhaps something else ran on the node at the same time. otherwise it is diff...
by bast
10 Mar 2014, 22:37
Forum: Running Dalton
Topic: Dalton Exits Without Any Errors
Replies: 6
Views: 7530

Re: Dalton Exits Without Any Errors

hi Jean, first of all i am pleased to see that apparently there exists a Dalton plugin for Avogadro which you have used? nice! for the problem i recommend that you first try to reduce the system. have you managed to get a similar system through? do you get the same crash with a smaller system? if si...
by bast
05 Mar 2014, 19:37
Forum: Installing Dalton
Topic: node/numa master error
Replies: 11
Views: 19314

Re: node/numa master error

hi Antonio,
i think the Dalton code is correct there (it should be integer*8) and that your 32-bit integer openmpi is strangely compiled.
please build the 32-bit integer openmpi like this:

Code: Select all

./configure CC=gcc CXX=g++ FC=gfortran F90=gfortran --prefix=/your/path
make all install
good luck,
radovan
by bast
05 Mar 2014, 15:09
Forum: Announcements
Topic: 2013.2 patch
Replies: 0
Views: 8336

2013.2 patch

Dear Dalton users, we have collected a number of fixes and improvements into the 2013.2 patch (changes are listed below). You can apply the patch in-place using the update.py script. After that you need to compile the changes: cd build make Alternatively you can download the 2013.2 version as a new ...
by bast
04 Mar 2014, 23:35
Forum: Installing Dalton
Topic: node/numa master error
Replies: 11
Views: 19314

Re: node/numa master error

also be careful with your math library. i doubt that your /usr/lib64/atlas libs understands 64-bit integers
unless it is specifically built for it. when using a 64-bit integer code calling 32-bit integer libraries anything can happen:
crashes, hangs, or simply wrong numbers.
by bast
04 Mar 2014, 23:18
Forum: Installing Dalton
Topic: node/numa master error
Replies: 11
Views: 19314

Re: node/numa master error

hi Antonio, you get many warnings but only one error and this seems to be the same problem as here: http://daltonprogram.org/forum/viewtopic.php?f=8&t=98 just looked into the code and i think you should change line 60 in DALTON/dft/general.h from void mpi_sync_data(const SyncData* data, int count); ...
by bast
04 Mar 2014, 20:50
Forum: Installing Dalton
Topic: node/numa master error
Replies: 11
Views: 19314

Re: node/numa master error

hi, so your MPI installation is now -fdefault-integer-8. this means that you have to compile the example with -fdefault-integer-8 otherwise the integer types do not match: mpifort -fdefault-integer-8 -g hello_usempi.f90 -o hello_usempi if you get the same errors from Dalton then it means that either...
by bast
03 Mar 2014, 09:55
Forum: Installing Dalton
Topic: node/numa master error
Replies: 11
Views: 19314

Re: node/numa master error

By the other hand, if I compile my openmpi with 64 bits integer support ./configure --prefix=/opt/openmpi-gnu/1.7.4 CFLAGS=-m64 CXXFLAGS=-m64 FFLAGS=-m64 FCFLAGS=-m64 --with-wrapper-cflags=-m64 --with-wrapper-cxxflags=-m64 --with-wrapper-fflags=-m64 --with-wrapper-fcflags=-m64 note that the above w...
by bast
02 Mar 2014, 19:43
Forum: Installing Dalton
Topic: error with ctest and exit code 139
Replies: 9
Views: 29121

Re: error with ctest and exit code 139

hi Hans, i just tested this on a as-similar-as-possible setup and was able to reproduce the error with: ifort/gcc/g++/int64 (your configuration) ifort/icc/icpc/int64 the calculation ran fine with: gfortran/gcc/g++/int64 ifort/gcc/g++ ifort/icc/icpc so the workaround for the moment is to either use G...
by bast
28 Feb 2014, 10:35
Forum: General discussions
Topic: starting coordinates
Replies: 2
Views: 6176

Re: starting coordinates

hi Rick, what i do for simple organic molecules is to build the molecule and pre-optimize it with Avogadro.
best regards,
radovan
by bast
21 Feb 2014, 17:33
Forum: General discussions
Topic: visualization software
Replies: 11
Views: 22189

Re: visualization software

hi Rick. i just implemented this as part of the very soon (hopefully next week) to be released 2013.2 patch.
by bast
21 Feb 2014, 08:53
Forum: General discussions
Topic: visualization software
Replies: 11
Views: 22189

Re: visualization software

i agree with you Erik - i will put it in.
by bast
20 Feb 2014, 23:27
Forum: Running Dalton
Topic: remote access to files
Replies: 8
Views: 9359

Re: remote access to files

it's no problem to transfer files. the local user support will tell you exactly how.
by bast
20 Feb 2014, 22:25
Forum: Running Dalton
Topic: remote access to files
Replies: 8
Views: 9359

Re: remote access to files

this is certainly possible but this forum is not the right place to ask this question because we don't know how things are set up at your cluster. you need to contact the local support for this. if you connect from a windows computer you probably connect using putty. in this case you can transfer fi...
by bast
20 Feb 2014, 21:14
Forum: General discussions
Topic: visualization software
Replies: 11
Views: 22189

Re: visualization software

hi Rick, i like the avogadro program: http://avogadro.cc/wiki/Main_Page it is cross platform and free. however, i am not aware of any program that reads Dalton output files directly. in the Dalton output you find the final geometry which is unfortunately printed in bohr and not in angstrom. in the l...
by bast
20 Feb 2014, 21:10
Forum: Running Dalton
Topic: remote access to files
Replies: 8
Views: 9359

Re: remote access to files

hi Carla,
do i understand correctly that you perhaps mean Dalton output files that are on some cluster? or what remote files do you mean?
radovan
by bast
20 Feb 2014, 15:55
Forum: General discussions
Topic: visualization software
Replies: 11
Views: 22189

Re: visualization software

hi Rick, what exactly do you want to do: look at molecules optimized by Dalton (in other words
post-processing)? or construct/visualize molecules that you then want to input into Dalton?
best greetings,
radovan
by bast
13 Feb 2014, 23:13
Forum: Installing Dalton
Topic: error with ctest and exit code 139
Replies: 9
Views: 29121

Re: error with ctest and exit code 139

dear Daniel, strange. make tests invokes ctest which invokes DALTON/test/TEST (or DALTON/test/test.pl). my worry is that the run fails in both cases but for some obscure reason "make test" manages to mark it as success. have never seen this. if i understood correctly, then any run fails if you execu...
by bast
13 Feb 2014, 22:21
Forum: Installing Dalton
Topic: error with ctest and exit code 139
Replies: 9
Views: 29121

Re: error with ctest and exit code 139

dear Daniel, that is a curious observation. "make test" is basically the same as "ctest". the only difference is that "make test" invokes "ctest --force-new-ctest-process" (see the generated Makefile; you could try that command directly just to see). i have never seen this problem. my suggestion is ...
by bast
03 Feb 2014, 17:34
Forum: Running Dalton
Topic: Modifying the Dalton script file with qsub
Replies: 11
Views: 12412

Re: Modifying the Dalton script file with qsub

i think the reason why you don't see any stdout/stderr is because you ask for "#PBS -k n" (keep none).
please remove this line.
also you don't need the very long path to your dal file.
add:
cd $PBS_O_WORKDIR
just before you call dalton.
by bast
03 Feb 2014, 16:57
Forum: Running Dalton
Topic: Modifying the Dalton script file with qsub
Replies: 11
Views: 12412

Re: Modifying the Dalton script file with qsub

ok that makes sense (the dal file).
please for testing start with less memory. increase only if you need to.
add to your script:
#PBS -e stderr.txt
#PBS -o stdout.txt
to get at least some information out why things failed.
by bast
03 Feb 2014, 16:27
Forum: Running Dalton
Topic: Modifying the Dalton script file with qsub
Replies: 11
Views: 12412

Re: Modifying the Dalton script file with qsub

isn't your dalton script in /home/doudou/Programs/Dalton2013/build/dalton instead of /home/doudou/Programs/Dalton2013/./dalton ? also note that you allocate 40 GB RAM per MPI process (so in total 240 GB RAM) - unless you have a big-RAM machine this will most probably immediately crash. i would not c...
by bast
03 Feb 2014, 15:12
Forum: Running Dalton
Topic: Modifying the Dalton script file with qsub
Replies: 11
Views: 12412

Re: Modifying the Dalton script file with qsub

i agree with Daniel. the standard approach to this is to not modify the dalton script but to call the dalton script
from within typically a bash script that contains some PBS directives understood by Torque.
John, please post your actual script so that we can check and correct it.
by bast
02 Feb 2014, 23:09
Forum: Installing Dalton
Topic: CMake Not Detecting MKL on Systems
Replies: 6
Views: 10145

Re: CMake Not Detecting MKL on Systems

more explicitly you should use:

Code: Select all

export MATH_ROOT=/opt/intel/mkl
./setup --mpi
cd build
make
by bast
02 Feb 2014, 23:07
Forum: Installing Dalton
Topic: CMake Not Detecting MKL on Systems
Replies: 6
Views: 10145

Re: CMake Not Detecting MKL on Systems

ok the reason why this can't work is that the -mkl flag only works with Intel compilers. we will improve documentation to make it more clear. since you use the GNU compiler, you should set MATH_ROOT (you have done that correctly) but NOT use --mkl=sequential. in short for GNU you have to use MATH_RO...