So, as seen in the previous post, mpich2 ver 1.4 and nwchem 6.0 don't play nicely together.
Continuing with the virtual machine in the previous post, I added a line referencing the stable version to /etc/apt/sources.list:
deb ftp://ftp.au.debian.org/debian/ stable main contrib non-free
Important: I ADDED that line -- all lines referencing the testing version (or wheezy) are left untouched.
Do
sudo apt-get update
Since the versions in stable are older adding that line won't affect your system.
Now,
apt-cache showpkg mpich2
Under provides it should say:
1.4.1-1+b1
1.2.1.1-5
Now,
sudo apt-get install mpich2=1.2.1.1-5
You'll get a warning that you're about to downgrade, which is what we're trying to do.
sudo apt-get autoremove (will downgrade dependent packages. Just go with it)
aptitude search mpich2
check what's installed and what version
aptitude show libmpich2-dev
If it's 1.4.1 or not installed, make sure to set it to 1.2.1.1-5 just like for mpich2
Run sh myconfig.sh (see here for the script). Seems to build ok. All the mpd tools are where they should be.
NOTE: according to this post mpd isn't needed in newer (>=1.3) versions.
In summary, this seems to be the way to build nwchem on wheezy -- by downgrading the mpich2 and mpich2-dev packages. Since downgrading those packages may affect other packages as well, it may cause problems, but so far so good.
Testing the built binary:
mpd --ncpus=4 &
mptrace -l
mpdrun -n 4 ./nwchem ../../examples/dirdyvtst/h3/h3tr1.nw
All is good
EDIT (16/12/2011):
So, you've installed an older version of a package. apt-get will want to upgrade it, so you should put the packages on 'hold'. Every time you upgrade your system apt-get will warn you that there are packages on hold, so don't worry about forgetting about it
sudo su
echo "mpich2 hold"|dpkg --set-selections
echo "libmpich2-dev hold"|dpkg --set-selections
(taken from http://forums.debian.net/viewtopic.php?f=20&t=71448&start=15)
As an aside, you may want to downgrade gromacs-mpich to use mpich2-1.2 as well:
sudo apt-get install gromacs-mpich=4.0.7-3
Lindqvist - a blog about Linux and Science. Mostly.
15 December 2011
28. Compiling/Building nwchem with mpich on debian 64 bit (15/12/2011) -- observations of squeeze, wheezy, sid and experimental
** NOTE: the nwchem build in the debian repos (6.0-1) does not support mpich. It will not run in parallel. It seems like 6.0-2 will, but it's not in the repos yet, and looking at the package status page I get a bit worried about the likelihood of seeing a finished build for amd64 **
** The solution to building on debian testing and above (and presumably ubuntu >10.10) is here: http://verahill.blogspot.com/2011/12/building-nwchem-on-debian-testing-64.html **
** NOTE: according to this post mpd isn't needed in newer (>=1.3) versions. It is needed -- and provided -- by mpich2 1.2**
So, I've had problems building nwchem on debian testing for about a year now. Actually, building nwchem is pretty straightforward, but building it with mpich2 support doesn't seem to work.
I also noted that mpd doesn't refer to an mpich daemon anymore, leading me to suspect that maybe the version of mpich2 (now at 1.4; was at 1.2 when I built on ubuntu early in the year) could be part of the problem.
Long story short: it builds with mpich2 support on debian stable (squeeze), but not debian testing (wheezy).
----------------------------------
SQUEEZE
----------------------------------
Here's what I did: I installed debian stable 64 bit in virtualbox from the business-card iso (standard tools + ssh. No desktop environment). I made sure the system (squeeze) was up to date, downloaded nwchem-6.0 and extracted it in /home/myhome/nwchem/nwchem-6.0 and create a build file, myconfig.sh, with the following content:
export LARGE_FILES=TRUE
export TCGRSH=/usr/local/bin/ssh
export NWCHEM_TOP=/home/myhome/nwchem/nwchem-6.0
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export MPI_LOC=/usr
export MPI_INCLUDE=$MPI_LOC/include/mpich2
export LIBMPI="-lfmpich -lmpich"
cd $NWCHEM_TOP/src
make nwchem_config
make FC=gfortran
Only thing remaining before building is:
sudo apt-get install mpich2 gfortran
mpich2: version 1.2
sh myconfig.sh then starts the build process which takes about 10-20 minutes in a virtual machine. Everything good. Works as should -- I only have one core in the virtual machine, so can't do much testing. It builds without a hitch though. In addition mpd, mpdtrace etc are all present.
Time to take a snapshot. 1.7 Gb.
----------------------------------
WHEEZY
----------------------------------
I next edited /etc/apt/sources.list and replaced all instances of squeeze with wheezy (including commenting out the last two lines (wheezey-updates / squeeze-updates), did sudo apt-get update and sudo apt-get dist-upgrade
mpich2: version 1.4.1.
mpd and mpdtrace are now gone. Only mpi* around.
Tried sh myconfig.sh again (added a make clean before make nwchem_config). It builds for a long time - 10-20 minutes -- ultimately the build fails with
..
..
/usr/lib/libmpich.so: undefined reference to `MPL_trid'
..
..
/usr/lib/libmpich.so: undefined reference to `MPL_trinit'
collect2: ld returned 1 exit status
make: *** [all] Error 1
The undefined references are: MPL_trid, MPL_trvalid, MPL_env2int, MPL_trrealloc, MPL_trspace, MPL_trDebugLevel, MPL_TrSetMaxMem, MPL_trlevel, MPL_trmalloc, MPL_putenv, MPL_env2bool, MPL_env2range, MPL_trcalloc, MPL_trfree, MPL_en2str, MPL_trstrdup, MPL_trdump and MPL_trinit
So no luck with Wheezy, which is the system I run on all my computers. I've actually tried quite a few approaches under Wheezy and have managed to complete the odd build, but without getting proper functionality i.e. using mpiexec -n 6 six instances are created instead of one instance spread across six cores so that the system is solved six times instead of just one.
----------------------------------
SID.
----------------------------------
Time to take another snapshot followed by an upgrade.
The wheezy snapshot is 2.2 Gb -- wonder where the 0.5 Gb come from?
Replacing all instances of wheezy with sid using vim (:%s/wheezy/sid/g). Fails to fetch http://security.debian.org/dists/sid/updates/main/binary-amd64/Packages during sudo apt-get update. Oh well. Remove that line from sources.list. Now update works.
Then sudo apt-get dist-upgrade. 140 Mb of archives to get.
As a general thought -- maybe it'd be worth keeping a copy of sid in a virtual machine just to see what's around the corner?
Upgrade done, sudo shutdown -r now
mpich2: version 1.4.1, same as wheezy. No mpd or mpdtrace.
Try building and...starts at 14:17, fails at 14:45. Same errors as for Wheezy.
Last chance -- snapshot (1.9 Gb...), add a ref to experimental and...no updates. They are the same. Not worth trying thus.
------------------------------------
So there you go -- nwchem builds ok on Squeeze using mpich2 ver 1.2, but not on any of the more up-to-date distros. I also wonder about the lack of mpd/mpdtrace -- in Squeeze mpd is the mpich daemon, while in Wheezy and above it's the Music Player Daemon. Something is odd here.
Coming next: can you build nwchem on Wheezy if you pull mpich2 ver 1.2 from the archives? Of course you can. The answer and how-to is here: http://verahill.blogspot.com/2011/12/building-nwchem-on-debian-testing-64.html
** The solution to building on debian testing and above (and presumably ubuntu >10.10) is here: http://verahill.blogspot.com/2011/12/building-nwchem-on-debian-testing-64.html **
** NOTE: according to this post mpd isn't needed in newer (>=1.3) versions. It is needed -- and provided -- by mpich2 1.2**
I also noted that mpd doesn't refer to an mpich daemon anymore, leading me to suspect that maybe the version of mpich2 (now at 1.4; was at 1.2 when I built on ubuntu early in the year) could be part of the problem.
Long story short: it builds with mpich2 support on debian stable (squeeze), but not debian testing (wheezy).
----------------------------------
SQUEEZE
----------------------------------
Here's what I did: I installed debian stable 64 bit in virtualbox from the business-card iso (standard tools + ssh. No desktop environment). I made sure the system (squeeze) was up to date, downloaded nwchem-6.0 and extracted it in /home/myhome/nwchem/nwchem-6.0 and create a build file, myconfig.sh, with the following content:
export LARGE_FILES=TRUE
export TCGRSH=/usr/local/bin/ssh
export NWCHEM_TOP=/home/myhome/nwchem/nwchem-6.0
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export MPI_LOC=/usr
export MPI_INCLUDE=$MPI_LOC/include/mpich2
export LIBMPI="-lfmpich -lmpich"
cd $NWCHEM_TOP/src
make nwchem_config
make FC=gfortran
Only thing remaining before building is:
sudo apt-get install mpich2 gfortran
mpich2: version 1.2
sh myconfig.sh then starts the build process which takes about 10-20 minutes in a virtual machine. Everything good. Works as should -- I only have one core in the virtual machine, so can't do much testing. It builds without a hitch though. In addition mpd, mpdtrace etc are all present.
Time to take a snapshot. 1.7 Gb.
----------------------------------
WHEEZY
----------------------------------
I next edited /etc/apt/sources.list and replaced all instances of squeeze with wheezy (including commenting out the last two lines (wheezey-updates / squeeze-updates), did sudo apt-get update and sudo apt-get dist-upgrade
mpich2: version 1.4.1.
mpd and mpdtrace are now gone. Only mpi* around.
Tried sh myconfig.sh again (added a make clean before make nwchem_config). It builds for a long time - 10-20 minutes -- ultimately the build fails with
..
..
/usr/lib/libmpich.so: undefined reference to `MPL_trid'
..
..
/usr/lib/libmpich.so: undefined reference to `MPL_trinit'
collect2: ld returned 1 exit status
make: *** [all] Error 1
The undefined references are: MPL_trid, MPL_trvalid, MPL_env2int, MPL_trrealloc, MPL_trspace, MPL_trDebugLevel, MPL_TrSetMaxMem, MPL_trlevel, MPL_trmalloc, MPL_putenv, MPL_env2bool, MPL_env2range, MPL_trcalloc, MPL_trfree, MPL_en2str, MPL_trstrdup, MPL_trdump and MPL_trinit
So no luck with Wheezy, which is the system I run on all my computers. I've actually tried quite a few approaches under Wheezy and have managed to complete the odd build, but without getting proper functionality i.e. using mpiexec -n 6 six instances are created instead of one instance spread across six cores so that the system is solved six times instead of just one.
----------------------------------
SID.
----------------------------------
Time to take another snapshot followed by an upgrade.
The wheezy snapshot is 2.2 Gb -- wonder where the 0.5 Gb come from?
Replacing all instances of wheezy with sid using vim (:%s/wheezy/sid/g). Fails to fetch http://security.debian.org/dists/sid/updates/main/binary-amd64/Packages during sudo apt-get update. Oh well. Remove that line from sources.list. Now update works.
Then sudo apt-get dist-upgrade. 140 Mb of archives to get.
As a general thought -- maybe it'd be worth keeping a copy of sid in a virtual machine just to see what's around the corner?
Upgrade done, sudo shutdown -r now
mpich2: version 1.4.1, same as wheezy. No mpd or mpdtrace.
Try building and...starts at 14:17, fails at 14:45. Same errors as for Wheezy.
Last chance -- snapshot (1.9 Gb...), add a ref to experimental and...no updates. They are the same. Not worth trying thus.
------------------------------------
So there you go -- nwchem builds ok on Squeeze using mpich2 ver 1.2, but not on any of the more up-to-date distros. I also wonder about the lack of mpd/mpdtrace -- in Squeeze mpd is the mpich daemon, while in Wheezy and above it's the Music Player Daemon. Something is odd here.
Coming next: can you build nwchem on Wheezy if you pull mpich2 ver 1.2 from the archives? Of course you can. The answer and how-to is here: http://verahill.blogspot.com/2011/12/building-nwchem-on-debian-testing-64.html
11 December 2011
27. Linux: some applications
Here are some linux tools which I've found myself using:
_Terminal/cli_:
email -- mutt
chat -- mcabber
spreadsheet -- sc, sed + gawk, python
calculator -- bc
editing -- vim, nano
browser -- elinks
music -- cplay
plotting -- gnuplot
maths -- octave, maxima
Gnome (some of these I use only in the terminal, so I list them twice):
terminal -- guake
latex -- gvim, texmaker, latexilla
editing -- gvim, gedit
plotting -- gnuplot
maths -- octave, maxima
system stats -- conky
email -- evolution
chat -- gajim
browser -- chrome
video -- vlc
music -- mostly cplay in cli, but otherwise vlc
crypto -- truecrypt
password management -- keepassx
I probably spend 90% of my time using vim since, being a 'simple' editor, it's so versatile. Before taking the time to learn vim, I used gedit (and to a smaller extent nano) for the same purpose. Nano is fine, but vim is more ubiquitous (in the form of vi) and has an excellent tutorial included. I simply don't know what the full capabilities of nano are -- maybe it's only as powerful as, say, notepad, or maybe it can do everything vim can.
I gave emacs a serious try about a year ago, and it didn't suit me. I do appreciate that emacs can be considered as an OS almost in itself, but since I believe in the idea of one program - one task, and find vim more user-friendly (not meaning learner-friendly, although it is too) I felt more motivated to get serious with vim. Two weeks with emacs brought me to the same level as two rather relaxed evenings with vim.
_Terminal/cli_:
email -- mutt
chat -- mcabber
spreadsheet -- sc, sed + gawk, python
calculator -- bc
editing -- vim, nano
browser -- elinks
music -- cplay
plotting -- gnuplot
maths -- octave, maxima
Gnome (some of these I use only in the terminal, so I list them twice):
terminal -- guake
latex -- gvim, texmaker, latexilla
editing -- gvim, gedit
plotting -- gnuplot
maths -- octave, maxima
system stats -- conky
email -- evolution
chat -- gajim
browser -- chrome
video -- vlc
music -- mostly cplay in cli, but otherwise vlc
crypto -- truecrypt
password management -- keepassx
I probably spend 90% of my time using vim since, being a 'simple' editor, it's so versatile. Before taking the time to learn vim, I used gedit (and to a smaller extent nano) for the same purpose. Nano is fine, but vim is more ubiquitous (in the form of vi) and has an excellent tutorial included. I simply don't know what the full capabilities of nano are -- maybe it's only as powerful as, say, notepad, or maybe it can do everything vim can.
I gave emacs a serious try about a year ago, and it didn't suit me. I do appreciate that emacs can be considered as an OS almost in itself, but since I believe in the idea of one program - one task, and find vim more user-friendly (not meaning learner-friendly, although it is too) I felt more motivated to get serious with vim. Two weeks with emacs brought me to the same level as two rather relaxed evenings with vim.
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