433. Wine 1.5.31 on Debian

Here's a generic way of building wine which works for 1.5.31 (and 1.5.28 and everything in between except 1.5.31).

See here for information about 3D acceleration using libGL/U with Wine: http://verahill.blogspot.com.au/2013/05/429-briefly-wine-libglliubglu-blender.html

Getting started:
If you set up a e.g. chroot to build 1.5.28 before, you don't need to set up a new chroot to build 1.5.31. In that case, skip the set-up step below and instead re-enter your existing chroot like this:

sudo mount -o bind /proc wine32/proc
sudo cp /etc/resolv.conf wine32/etc/resolv.conf
sudo chroot wine32
su sandbox

cd ~/tmp

Setting up the Chroot

sudo apt-get install debootstrap
mkdir $HOME/tmp/architectures/wine32 -p
cd $HOME/tmp/architectures
sudo debootstrap --arch i386 wheezy $HOME/tmp/architectures/wine32 http://ftp.au.debian.org/debian/
sudo mount -o bind /proc wine32/proc
sudo cp /etc/resolv.conf wine32/etc/resolv.conf
sudo chroot wine32

You're now in the chroot:

apt-get update
apt-get install locales sudo vim
echo 'export LC_ALL="C"'>>/etc/bash.bashrc
echo 'export LANG="C"'>>/etc/bash.bashrc
echo '127.0.0.1 localhost beryllium' >> /etc/hosts
source /etc/bash.bashrc
adduser sandbox
usermod -g sudo sandbox
echo 'Defaults !tty_tickets' >> /etc/sudoers
su sandbox
cd ~/

Replace 'beryllium' with the name your host system (it's just to suppress error messages)

---

Building Wine
While still in the chroot, continue (the i386 is ok; don't worry about it -- you don't actually need it):

sudo apt-get install libx11-dev:i386 libfreetype6-dev:i386 libxcursor-dev:i386 libxi-dev:i386 libxxf86vm-dev:i386 libxrandr-dev:i386 libxinerama-dev:i386 libxcomposite-dev:i386 libglu-dev:i386 libosmesa-dev:i386 libglu-dev:i386 libosmesa-dev:i386 libdbus-1-dev:i386 libgnutls-dev:i386 libncurses-dev:i386 libsane-dev:i386 libv4l-dev:i386 libgphoto2-2-dev:i386 liblcms-dev:i386 libgstreamer-plugins-base0.10-dev:i386 libcapi20-dev:i386 libcups2-dev:i386 libfontconfig-dev:i386 libgsm1-dev:i386 libtiff-dev:i386 libpng-dev:i386 libjpeg-dev:i386 libmpg123-dev:i386 libopenal-dev:i386 libldap-dev:i386 libxrender-dev:i386 libxml2-dev:i386 libxslt-dev:i386 libhal-dev:i386 gettext:i386 prelink:i386 bzip2:i386 bison:i386 flex:i386 oss4-dev:i386 checkinstall:i386 ocl-icd-libopencl1:i386 opencl-headers:i386 libasound2-dev:i386 build-essential

mkdir ~/tmp
cd ~/tmp
wget http://prdownloads.sourceforge.net/wine/wine-1.5.31.tar.bz2
tar xvf wine-1.5.31.tar.bz2
cd wine-1.5.31/./configure
time make -j3
sudo checkinstall --install=no

checkinstall 1.6.2, Copyright 2009 Felipe Eduardo Sanchez Diaz Duran
           This software is released under the GNU GPL.


The package documentation directory ./doc-pak does not exist. 
Should I create a default set of package docs?  [y]: 

Preparing package documentation...OK

Please write a description for the package.
End your description with an empty line or EOF.
>> wine 1.5.31
>> 

*****************************************
**** Debian package creation selected ***
*****************************************

This package will be built according to these values: 

0 -  Maintainer: [ root@beryllium ]
1 -  Summary: [ wine 1.5.31]
2 -  Name:    [ wine ]
3 -  Version: [ 1.5.31]
4 -  Release: [ 1 ]
5 -  License: [ GPL ]
6 -  Group:   [ checkinstall ]
7 -  Architecture: [ i386 ]
8 -  Source location: [ wine-1.5.31 ]
9 -  Alternate source location: [  ]
10 - Requires: [  ]
11 - Provides: [ wine ]
12 - Conflicts: [  ]
13 - Replaces: [  ]

Checkinstall takes a little while (In particular this step: 'Copying files to the temporary directory...').

---

Installing Wine

Exit the chroot

sandbox@beryllium:~/tmp/wine-1.5.31$ exit
exit
root@beryllium:/# exit
exit
me@beryllium:~/tmp/architectures$ 

On your host system
 Enable multiarch* and install ia32-libs, since you've built a proper 32 bit binary:

sudo dpkg --add-architecture i386
sudo apt-get update
sudo apt-get install ia32-libs

*At some point I think ia32-libs may be replaced by proper multiarch packages, but maybe not. So we're kind of doing both here.

 Copy the .deb package and install it

sudo cp wine32/home/sandbox/tmp/wine-1.5.31/wine_1.5.31-1_i386.deb .
sudo chown $USER wine_1.5.31-1_i386.deb
sudo dpkg -i wine_1.5.31-1_i386.deb

---

Links to this post:
http://appdb.winehq.org/objectManager.php?sClass=version&iId=19141&iTestingId=79415&bShowAll=true

432. NWChem 6.3 -- COSMO is now fast(er)!

I probably would've been more excited about this about a year ago when I 'believed' in implicit solvation models (nothing's perfect, and we'll use what is practical so they do fill a strong need. They just aren't very informative for a lot of systems) but it's still a Good Thing.

COSMO has been done using numerical gradients in nwchem 6.1.1 and earlier versions, which has meant that it's been horrendously slow in many cases, in particular if you need to optimise a structure using implicit solvation. COSMO has been -- and still is -- the only implicit solvation model implemented in NWChem, so slow COSMO puts a bit of a spanner in the solvation energy works. Sometimes the calculation even refuses to converge at all.

In contrast, Gaussian has had a number of implicit solvation models implemented, ranging from the quick and dirty PCM, to slower (and better?) C-PCM and I-PCM.

So this is great news.

A quick example:

---

The test:
Here's a test job (the default cosmo parameters aren't realistic, but this is for testing purposes):

scratch_dir /scratch
start benzene 

geometry units angstroms
C  0.100  1.396  0.000
C  1.209  0.698  0.000
C  1.209 -0.698  0.000
C  0.000 -1.396  0.000
C -1.209 -0.698  0.000
C -1.209  0.698  0.000
H  0.000  2.479  0.000
H  2.147  1.240  0.000
H  2.147 -1.240  0.000
H  0.000 -2.479  0.000
H -2.147 -1.240  0.000
H -2.147  1.240  0.000
end

basis
 H library "6-31+g*" 
 c library "6-31+g*"
end
dft
        direct
end
cosmo
end

scf
        maxiter 999
end

task dft

Note that this is the same test job (plus cosmo, minus optimize) as shown here: http://verahill.blogspot.com.au/2013/05/430-briefly-crude-comparison-of.html

---

The results:
And here is what I see using nwchem 6.3. (w/ acml 5.3.1, AMD FX 8150/32 gb ram):

6.1.1 19.4 seconds
6.3   14.3 seconds

The difference isn't significant (in the sense that times are too variable so we can't really tell which is faster for such a short job).

But when we change task dft to task dft optimize we get

6.1.1 Fails after 2600 seconds
6.3   128.3 seconds

6.3 churns through the steps pretty efficiently:

@ Step       Energy      Delta E   Gmax     Grms     Xrms     Xmax   Walltime
@ ---- ---------------- -------- -------- -------- -------- -------- --------
@    0    -230.09337488  0.0D+00  0.07376  0.01302  0.00000  0.00000     18.1
@    1    -230.10523734 -1.2D-02  0.00903  0.00231  0.03627  0.10509     45.7
@    2    -230.10619442 -9.6D-04  0.00491  0.00084  0.01898  0.06082     69.1
@    3    -230.10628696 -9.3D-05  0.00176  0.00030  0.00737  0.02428     93.3
@    4    -230.10629787 -1.1D-05  0.00023  0.00005  0.00219  0.00682    115.8
@    5    -230.10629827 -4.0D-07  0.00004  0.00001  0.00047  0.00136    128.2
@    5    -230.10629827 -4.0D-07  0.00004  0.00001  0.00047  0.00136    128.2

while 6.1.1 drags itself along for almost an hour:

@ Step       Energy      Delta E   Gmax     Grms     Xrms     Xmax   Walltime
@ ---- ---------------- -------- -------- -------- -------- -------- --------
@    0    -230.09389924  0.0D+00  0.07389  0.01306  0.00000  0.00000    691.4
@    1    -230.10680306 -1.3D-02  0.01081  0.00197  0.03065  0.10438   1378.3
@    2    -230.10690186 -9.9D-05  0.01000  0.00167  0.00231  0.00803   2092.2

before failing with

6:6:driver: task_gradient failed:: 0
(rank:6 hostname:neon pid:4536):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/armci.c:ARMCI_Error():208 cond:0
 ------------------------------------------------------------------------
 There is an error related to the specified geometry
 ------------------------------------------------------------------------

Sure, the optimization takes 128 seconds instead of ca 44 seconds, but for anyone who's used NWCHEM with COSMO in the past, that's actually not too bad.

I ran another job to get a better feeling for how much longer COSMO vs no COSMO takes for optimization. Optimization of Arecoline (available in ECCE as a fragment) at rb3lyp/6-31+G* takes 2h 5 min with COSMO (33 optimization steps). Without COSMO it takes 37 minutes and uses 14 steps.

431. Briefly: a crude comparison of performance of NWChem 6.1, 6.1.1 and 6.3.

Just a simple comparison of different versions of nwchem on different hardware. It's mostly interesting to myself as a general guide to how slow my nodes are in relative terms.

I built nwchem as shown here: http://verahill.blogspot.com.au/2013/05/424-nwchem-63-on-debian-wheezy.html
and openblas as shown here: http://verahill.blogspot.com.au/2013/05/423-openblas-on-debian-wheezy.html
and installed acml as shown here: http://verahill.blogspot.com.au/2013/05/422-set-up-acml-on-linux.html

I'm using ECCE: http://verahill.blogspot.com.au/2013/01/325-compiling-ecce-64-on-debian-testing.html
and SGE: http://verahill.blogspot.com.au/2012/06/setting-up-sun-grid-engine-with-three.html
I've set up ECCE similarly to what is shown here: http://verahill.blogspot.com.au/2012/06/ecce-in-virtual-machine-step-by-step.html

---

Test job:

scratch_dir /scratch
Title "opt freq"

Start  biphenyl_cation_twisted

echo

charge 1

geometry autosym units angstrom
 C     0.00000     -3.56301     0.00000
 C     -1.13927     -2.85928     -0.393841
 C     -1.13879     -1.46545     -0.394153
 C     0.00000     -0.742814     0.00000
 C     1.13879     -1.46545     0.394153
 C     1.13927     -2.85928     0.393841
 C     0.00000     0.742814     0.00000
 C     1.13879     1.46545     -0.394153
 C     1.13927     2.85928     -0.393841
 C     -1.13879     1.46545     0.394153
 C     0.00000     3.56301     0.00000
 C     -1.13927     2.85928     0.393841
 H     0.00000     -4.64896     0.00000
 H     -2.02827     -3.39662     -0.711607
 H     -2.02148     -0.928265     -0.727933
 H     2.02827     -3.39662     0.711607
 H     2.02827     3.39662     -0.711607
 H     -2.02148     0.928265     0.727933
 H     0.00000     4.64896     0.00000
 H     -2.02827     3.39662     0.711607
 H     2.02148     0.928265     -0.727933
 H     2.02148     -0.928265     0.727933
end

ecce_print ecce.out

basis "ao basis" cartesian print
  H library "6-31G**"
  C library "6-31G**"
END

dft
  mult 2
  XC b3lyp
  mulliken
end

driver
end

task dft optimize
task dft freq numerical

---

Results:
The jobs were run using all cores available.

AMD Phenom II X6 1055T, 8 Gb RAM, Openblas. Six cores.

6.1    2461
6.1.1  2114
6.3    2044
6.3    2048**

**using MKL compiled with ifort (http://verahill.blogspot.com.au/2013/07/469-intel-compiler-on-debian.html).

AMD FX 8150, 32 Gb RAM, acml 5.3.1 (gfortran, int64, fma4) -- earlier versions of nwchem were compiled against different versions of acml. Eight cores.

6.1    1619s
6.1.1  1588s
6.3    1611s
6.3    1507s**

**using MKL compiled with ifort (http://verahill.blogspot.com.au/2013/07/469-intel-compiler-on-debian.html).

Intel i5-2400, 16 Gb RAM, openblas. Four cores.

6.1    1689s
6.1.1  1696s
6.3    1652s
6.3    1550s*
6.3    1498s**

*using Intel MKL (see http://verahill.blogspot.com.au/2013/06/465-intel-mkl-math-kernel-library-on.html)
**using MKL compiled with ifort (http://verahill.blogspot.com.au/2013/07/469-intel-compiler-on-debian.html).

AMD Athlon II X3, 4 gb RAM, acm 5.3.1. Three cores.

6.3    4818s 
6.3    4058s**

**using MKL compiled with ifort (http://verahill.blogspot.com.au/2013/07/469-intel-compiler-on-debian.html).