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.

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!

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.