[ase-users] Jacapo/Dacapo not working on Ubuntu 11.04
Alex Eftimiades
alexeftimiades at gmail.com
Thu Aug 25 15:32:10 CEST 2011
Yes, that thread is where I got the idea of removing option.
gfortran and mpi were installed via apt-get.
gfortran -v:
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/lib/i386-linux-gnu/gcc/i686-linux-gnu/4.5.2/lto-wrapper
Target: i686-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro
4.5.2-8ubuntu4' --with-bugurl=file:///usr/share/doc/gcc-4.5/README.Bugs
--enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
--program-suffix=-4.5 --enable-shared --enable-multiarch
--with-multiarch-defaults=i386-linux-gnu --enable-linker-build-id
--with-system-zlib --libexecdir=/usr/lib/i386-linux-gnu
--without-included-gettext --enable-threads=posix
--with-gxx-include-dir=/usr/include/c++/4.5 --libdir=/usr/lib/i386-linux-gnu
--enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug
--enable-libstdcxx-time=yes --enable-plugin --enable-gold
--enable-ld=default --with-plugin-ld=ld.gold --enable-objc-gc
--enable-targets=all --disable-werror --with-arch-32=i686
--with-tune=generic --enable-checking=release --build=i686-linux-gnu
--host=i686-linux-gnu --target=i686-linux-gnu
Thread model: posix
gcc version 4.5.2 (Ubuntu/Linaro 4.5.2-8ubuntu4)
ompi_info | head -50:
Package: Open MPI buildd at roseapple Distribution
Open MPI: 1.4.3
Open MPI SVN revision: r23834
Open MPI release date: Oct 05, 2010
Open RTE: 1.4.3
Open RTE SVN revision: r23834
Open RTE release date: Oct 05, 2010
OPAL: 1.4.3
OPAL SVN revision: r23834
OPAL release date: Oct 05, 2010
Ident string: 1.4.3
Prefix: /usr
Configured architecture: i686-pc-linux-gnu
Configure host: roseapple
Configured by: buildd
Configured on: Fri Jan 7 06:05:46 UTC 2011
Configure host: roseapple
Built by: buildd
Built on: Fri Jan 7 06:12:03 UTC 2011
Built host: roseapple
C bindings: yes
C++ bindings: yes
Fortran77 bindings: yes (all)
Fortran90 bindings: yes
Fortran90 bindings size: small
C compiler: gcc
C compiler absolute: /usr/bin/gcc
C++ compiler: g++
C++ compiler absolute: /usr/bin/g++
Fortran77 compiler: gfortran
Fortran77 compiler abs: /usr/bin/gfortran
Fortran90 compiler: gfortran
Fortran90 compiler abs: /usr/bin/gfortran
C profiling: yes
C++ profiling: yes
Fortran77 profiling: yes
Fortran90 profiling: yes
C++ exceptions: no
Thread support: posix (mpi: no, progress: no)
Sparse Groups: no
Internal debug support: no
MPI parameter check: runtime
Memory profiling support: no
Memory debugging support: no
libltdl support: yes
Heterogeneous support: yes
mpirun default --prefix: no
MPI I/O support: yes
MPI_WTIME support: gettimeofday
Symbol visibility support: yes
On Thu, Aug 25, 2011 at 4:05 AM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>wrote:
> Hi,
>
> this looks like:
> http://forum.wrfforum.com/**viewtopic.php?f=5&t=1501<http://forum.wrfforum.com/viewtopic.php?f=5&t=1501>
> Can you post:
> gfortran -v
> and
> ompi_info | head -50
>
> Marcin
>
> Alex Eftimiades wrote:
>
>> I do not think the problem is not underscoring. I tried with
>> fsecond_underscore, and it would not compile.
>>
>> The serial version does compile without the patch. The mpi version does
>> not. It complains about -f90 being an "unrecognized option" an promptly
>> halts. With that option removed, in just complained noisily about some
>> unexpected tokens (I am going on memory--it has been a few weeks since I
>> compiled the code.)
>>
>> I have both working on my computer now. Here is the relevant section of
>> the installer script I use:
>>
>> cd /opt
>> svn checkout https://svn.fysik.dtu.dk/**projects/dacapo/trunk<https://svn.fysik.dtu.dk/projects/dacapo/trunk>dacapo
>> cd dacapo
>> mv psp psp2
>> mkdir psp
>> for m in `find ./psp2 -name '*.pseudo'`;do mv $m ./psp;done
>> rm -rf psp2
>> cd src
>> export NETCDF="/usr/lib"
>> export DACAPOPATH="/opt/dacapo/psp"
>> export BLASLAPACK="-L/usr/lib -lnetcdff -lnetcdf -L/usr/lib -lblas
>> -llapack -L/usr/lib -lblas -llapack -lgfortran"
>> export FFTW="/usr/lib"
>> export MPIDIR="/usr/lib/openmpi"
>> export MPI_LIBDIR="$MPIDIR/lib"
>> export MPI_INCLUDEDIR="$MPIDIR/**include"
>> export MPI_BINDIR="/usr/bin"
>> make gfortran_fnosecond_underscore
>> patch Makefile < ~/Downloads/dacapo_patch_for_**ubuntu.patch #This is a
>> simple patch I made that seems to allow the program to compile the mpi
>> version with gfortran
>> make gfortran_fnosecond_underscore MP=mpi
>> echo "
>> export DACAPOPATH=\"/opt/dacapo/psp\"
>> export PATH=\$PATH:/opt/dacapo/src/**gfortran_fnosecond_underscore_**serial
>> #For the mpi version, change serial to to mpi
>> " >> ~/.bashrc
>> . ~/.bashrc
>>
>>
>> This and the patch are posted here: http://sourceforge.net/**
>> projects/aeftimiamisc/files/**installstuff/<http://sourceforge.net/projects/aeftimiamisc/files/installstuff/>
>>
>> Dacapo works just fine in serial
>>
>> On Aug 24, 2011, at 12:18 PM, Marcin Dulak wrote:
>>
>> Hi,
>>>
>>> i think we need to split the problem into smaller ones:
>>> 1. please try to install the serial version of dacapo first.
>>> You should not need any patches - maybe the right underscoring
>>> conventions for you system is gfortran_fsecond_underscore
>>> and not gfortran_fnosecond_underscore. Please check you underscoring
>>> convention as described here https://listserv.fysik.dtu.dk/**
>>> pipermail/ase-users/2009-**September/000362.html<https://listserv.fysik.dtu.dk/pipermail/ase-users/2009-September/000362.html>
>>> 2. are you able to run the simple example CO from
>>> https://wiki.fysik.dtu.dk/ase/**ase/calculators/jacapo.html<https://wiki.fysik.dtu.dk/ase/ase/calculators/jacapo.html>
>>> ?
>>> To the problem of the optimizer I get in a separate post.
>>>
>>> Best regards,
>>>
>>> Marcin
>>>
>>> Alex Eftimiades wrote:
>>>
>>>> I am trying to run the unit cell optimization provided here:
>>>> http://gilgamesh.cheme.cmu.**edu/jacapo/jacapo/2-bulk/2.2-**
>>>> unitcell-optimization/2.2.0-**unit-cell-optimization.html<http://gilgamesh.cheme.cmu.edu/jacapo/jacapo/2-bulk/2.2-unitcell-optimization/2.2.0-unit-cell-optimization.html>
>>>>
>>>> I get:
>>>> >>> print bulk.get_stresses()
>>>> None
>>>>
>>>> That happens for all the examples on the page. Much worse errors occure
>>>> if I try bulk.get_forces()
>>>> File "<stdin>", line 1, in <module>
>>>> File "/usr/lib/python2.7/dist-**packages/ase/atoms.py", line 571, in
>>>> get_forces
>>>> forces = self._calc.get_forces(self)
>>>> File "/usr/lib/python2.7/dist-**packages/ase/calculators/**jacapo/jacapo.py",
>>>> line 2309, in get_forces
>>>> forces = nc.variables['**DynamicAtomForces'][-1]
>>>> KeyError: 'DynamicAtomForces'
>>>>
>>>> I should note I manually transcribed that error output (as well as the
>>>> ones described later in this message.) from another computer screen, so
>>>> please try to look over any typos.
>>>>
>>>> Now, I installed everything except decapo from apt-get repositories
>>>> (including ase and gpaw.) Decapo did not install willingly. Here is the
>>>> sequence of commands I used:
>>>> cd /opt
>>>> DIR=~/Downloads
>>>> svn checkout https://svn.fysik.dtu.dk/**projects/dacapo/trunk<https://svn.fysik.dtu.dk/projects/dacapo/trunk>dacapo
>>>> cd dacapo
>>>> mv psp psp2
>>>> mkdir psp
>>>> for m in `find ./psp2 -name '*.pseudo'`;do mv $m ./psp;done
>>>> rm -rf psp2
>>>> cd src
>>>> export NETCDF="/usr/lib"
>>>> export DACAPOPATH="/opt/dacapo/psp"
>>>> export BLASLAPACK="-L/usr/lib -lnetcdff -lnetcdf -L/usr/lib -lblas
>>>> -llapack -L/usr/lib -lblas -llapack -lgfortran"
>>>> export FFTW="/usr/lib"
>>>> export MPIDIR="/usr/lib/openmpi"
>>>> export MPI_LIBDIR="$MPIDIR/lib"
>>>> export MPI_INCLUDEDIR="$MPIDIR/**include"
>>>> export MPI_BINDIR="/usr/bin"
>>>> patch Makefile < $DIR/dacapo_patch_for_ubuntu.**patch.patch #This is a
>>>> simple patch I made that seems to allow the program to compile with gfortran
>>>> make gfortran_fnosecond_underscore MP=mpi
>>>> echo "
>>>> export PATH=\$PATH:/opt/dacapo/src/**gfortran_fnosecond_underscore_**
>>>> mpi
>>>> " >> ~/.bashrc
>>>> . ~/.bashrc
>>>> You can download the patch, dacapo_patch_for_ubuntu.patch.**patch,
>>>> from: http://sourceforge.net/**projects/aeftimiamisc/files/**
>>>> installstuff/dacapo_patch_for_**ubuntu.patch.patch/download<http://sourceforge.net/projects/aeftimiamisc/files/installstuff/dacapo_patch_for_ubuntu.patch.patch/download>
>>>> It deletes the compiler option -f90=$(GFORTRAN_FNOSECOND_**UNDERSCORE_FC90)'
>>>> MPI_LIBDIR=${GFORTRAN_**FNOSECOND_UNDERSCORE_MPIDIR}
>>>> which the mpi compiler does not recognize. I will try again with the
>>>> serial version tomorrow. In the mean time has anyone gotten this
>>>> successfully working on Ubuntu (recently.) I have looked through the
>>>> listserves and followed everything they suggested.
>>>>
>>>> *I really just need /something/ that can optimize the geometry and the
>>>> unit cell.* If anyone knows of any other (free) software that can do that,
>>>> please let me know!
>>>>
>>>>
>>>> Thanks,
>>>> Alex
>>>>
>>>>
>>>> warning: extra tokens at end of #endif directive
>>>> and Warning: Deleted feaure: End of expression in DO loop at (1) must be
>>>> integer
>>>>
>>>
>>>
>>> --
>>> *************************************
>>> Marcin Dulak
>>> Technical University of Denmark
>>> Department of Physics
>>> Building 307, Room 229
>>> DK-2800 Kongens Lyngby
>>> Denmark
>>> Tel.: (+45) 4525 3157
>>> Fax.: (+45) 4593 2399
>>> email: Marcin.Dulak at fysik.dtu.dk <mailto:Marcin.Dulak at fysik.**dtu.dk<Marcin.Dulak at fysik.dtu.dk>
>>> >
>>>
>>> *************************************
>>>
>>>
>>
>
> --
> *************************************
>
> Marcin Dulak
> Technical University of Denmark
> Department of Physics
> Building 307, Room 229
> DK-2800 Kongens Lyngby
> Denmark
> Tel.: (+45) 4525 3157
> Fax.: (+45) 4593 2399
> email: Marcin.Dulak at fysik.dtu.dk
>
> *************************************
>
>
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