Showing posts with label 32 bit. Show all posts
Showing posts with label 32 bit. Show all posts

24 February 2012

74. Building nwchem 6.1 on debian testing 32 bit only


EDIT 18 May 2012: 
It's now been solved on 64 bit as well
Compiling nwchem 6.1 with internal libs on debian: http://verahill.blogspot.com.au/2012/05/compiling-nwchem-61-with-internal-libs.html
Compiling nwchem 6.1 with openblas on debian: http://verahill.blogspot.com.au/2012/05/building-nwchem-61-on-debian.html


This doesn't work with the 64 bit version of nwchem 6.1. There's a separate post on that. Nwchem 6.1 64 bit will build just fine, but will crash when run. Again, see the other post.

Building on 32 bit debian testing:



Put a hold on your mpich2 and mpich2-dev packages (see e.g. here for more details)
1. edit your /etc/apt/sources.list to allow packages from stable e.g.

deb ftp://ftp.au.debian.org/debian/ testing main contrib non-fre
deb ftp://ftp.au.debian.org/debian/ stable main contrib non-free

2. create an /etc/apt/preferences file e.g.

Package: *
Pin: release a=testing
Pin-Priority: 990
Package: *
Pin: release a=stable
Pin-Priority: -10
2. install v 1.2 explicitly
sudo apt-get update && sudo apt-get install mpich2=1.2.1.1-5 libmpich2-dev=1.2.1.1-5

3. put a hold on the packages

sudo su
echo "mpich2 hold"|dpkg --set-selections
echo "libmpich2-dev hold"|dpkg --set-selections

exit

Make sure you have the necessary packages:
sudo apt-get install build-essential gfortran fort77

I had some error messages before installing fort77. Not sure they are related.

Download the nwchem source
cd ~
wget http://www.nwchem-sw.org/images/Nwchem-6.1-2012-Feb-10.tar.gz
tar -xvf Nwchem-6.1-2012-Feb.tar.gz
cd nwchem-6.1

create buildconf.sh in ~/nwchem-6.1


export LARGE_FILES=TRUE
export TCGRSH=/usr/local/bin/ssh
export NWCHEM_TOP=/home/me/nwchem-6.1
export NWCHEM_TARGET=LINUX
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/usr
export MPI_LIB=$MPI_LOC/lib
export MPI_INCLUDE=$MPI_LOC/include/mpich2
export LIBMPI="-lmpich -lfmpich -lpthread"
export NWCHEM_MODULES="all"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran

run
sh buildconf.sh


Building takes ages. But it works. Why it works for 32 bit and not 64 bit has me a bit confused, but it's probably a good hint to the solution.

08 February 2012

60. i18n_translation and no Package:Header error on Debian Testing 32 bit

I'm doing this via an apt-cache server (i.e. the 192.168.1.1 rather than ftp.au.debian.org) -- but the problem is unrelated to the apt-cache server.

Symptom:

Get:1 http://192.168.1.1 testing InRelease [179 kB]
Ign http://192.168.1.1 testing/contrib TranslationIndex
Get:2 http://192.168.1.1 testing/main TranslationIndex [2,154 B]
Ign http://192.168.1.1 testing/non-free TranslationIndex
Get:3 http://192.168.1.1 testing/main i386 Packages [7,146 kB]
Get:4 http://192.168.1.1 testing/contrib i386 Packages [48.9 kB]
Get:5 http://192.168.1.1 testing/non-free i386 Packages [87.5 kB]
Ign http://192.168.1.1 testing/contrib Translation-en_AU
Get:6 http://192.168.1.1 testing/contrib Translation-en [34.8 kB]
Get:7 http://192.168.1.1 testing/main Translation-en [3,722 kB]
Ign http://192.168.1.1 testing/non-free Translation-en_AU                                
Get:8 http://192.168.1.1 testing/non-free Translation-en [62.5 kB]
Fetched 11.3 MB in 2s (4,348 kB/s)                                                          
W: Failed to fetch copy:/var/lib/apt/lists/partial/192.168.1.1:3142_ftp.au.debian.org_debian_dists_testing_main_i18n_Translation-en  Encountered a section with no Package: header

E: Some index files failed to download. They have been ignored, or old ones used instead.

Reason:
ftp://ftp.au.debian.org/debian/dists/wheezy/main/i18n/
All the files in that directory are compressed (bz2) -- you need to enable apt-get to decompress .bz2 files.

Solution:
Install bzip2

sudo apt-get install bzip2

at this point gives

Reading package lists... Error!
E: Encountered a section with no Package: header
E: Problem with MergeList /var/lib/apt/lists/192.168.1.1:3142_ftp.au.debian.org_debian_dists_testing_contrib_i18n_Translation-en
E: The package lists or status file could not be parsed or opened.

So remove the offending files (2 lines):
sudo rm  /var/lib/apt/lists/192.168.1.1:3142_ftp.au.debian.org_debian_dists_testing_contrib_i18n_Translation-en
sudo rm /var/lib/apt/lists/192.168.1.1:3142_ftp.au.debian.org_debian_dists_testing_non-free_i18n_Translation-en

Now you can 

sudo apt-get install bzip2

followed by

sudo apt-get update
Hit http://192.168.1.1 testing InRelease
Get:1 http://192.168.1.1 testing/main i386 Packages/DiffIndex [2,038 B]
Get:2 http://192.168.1.1 testing/contrib i386 Packages/DiffIndex [2,023 B]
Get:3 http://192.168.1.1 testing/non-free i386 Packages/DiffIndex [2,023 B]
Ign http://192.168.1.1 testing/contrib TranslationIndex
Hit http://192.168.1.1 testing/main TranslationIndex
Ign http://192.168.1.1 testing/non-free TranslationIndex
Get:4 http://192.168.1.1 testing/contrib Translation-en [34.8 kB]
Get:5 http://192.168.1.1 testing/main Translation-en [3,722 kB]
Get:6 http://192.168.1.1 testing/non-free Translation-en [62.5 kB]
Ign http://192.168.1.1 testing/contrib Translation-en_AU        
Ign http://192.168.1.1 testing/non-free Translation-en_AU
Fetched 103 kB in 4s (25.3 kB/s)
Reading package lists... Done

Done indeed!

17 January 2012

49. Gromacs -- hangs on multicore when doing normal mode analysis

Symptom:
when doing
mdrun -s nm.tpr -mtx nm.mtx -v -deffnm nm
on a system with 637 atoms you end up with:
...Finish step 636 out of 637
and it hangs there with all cores running at 100%

Reason:
For some reason the normal mode analysis of at least this particular system won't run on multiple cores.

Solution:
Use an mpi compiled version of mdrun (see previous posts on compiling _dd, _mpi and _ddmpi versions of gromacs) and force the use of ONE core.

mpd --ncpus=4 &
mpdrun -n 1 mdrun_mpi -s nm.tpr -mtx nm.mtx -v -deffm nm

works!

Confirmation
This was confimed by running it on four computers:
64 bit: a six core AMD 64 using a compiled version of gromacs. Hangs.
64 bit: a four core intel i5 using both the debian version and a compiled version of gromacs. Hangs.
64 bit: an older four core intel using a compiled version of gromacs. Hangs.
32 bit: an old single-core laptop using the debian version of gromacs. Works.

Next, three single-core virtual machines were set up -- a stable 32 bit, a testing 32 bit and a testing 64 bit machine, all with the debian version of gromacs (sudo apt-get install gromac). They all worked, as they only had a single core.