Lindqvist -- a blog about Linux and Science. Mostly.

lindqvist

Update 19 Feb. 2013:
Here's an updated post: http://verahill.blogspot.com.au/2013/02/341-upgradinginstalling-bankid-on-64.html -- see that one instead, in particularly if you're upgrading.

Note that you may have to compile your own nspluginwrapper:
http://verahill.blogspot.com.au/2013/03/366-nspluginwrapper-on-debian.html

and you will need to enable multiarch to install ia32-libs:

sudo dpkg --add-architecture i386
sudo apt-get update

Original post:
Swedish banks and government institutions use bankid/nexus personal for electronic id verification. Sadly, it's a horrible solution -- it seems to be closed source, the bankid website is a POS which prevents me from downloading the 64 bit version claiming that it's not supported (I've used it for a few years now, so it's clearly bunkum).

Note that there's a FOSS alternative in Fribid (http://verahill.blogspot.se/2012/02/debian-testing-wheezy-64-fribid-as.html) which seems to be working perfectly -- and if you can use it, use it. The main limitation is that in practice you'll have to collect your certificate/ID with it, since newer versions of BankID saves the ID in an incompatible format. Like many foreigners, I don't have the opportunity to visit Sweden for the sole sake of picking up a new ID, so I'm stuck with BankID. But you may not be.

* A Swedish how-to is available here: http://ubuntu-se.org/wiki/NexusPersonal#Installation_p.C3.A5_64-bitarssystem

* Another, more recent how-to is here: http://popqvarnstrom.blogspot.com.au/2011/06/bankid-nexus-personal-on-ubuntu-1104-64.html

Note: I have never 'exported' my ID, but have always copied the ~/.personal directory between computers. The problem with exporting is that you are only allowed to do it once. The problem with Nexus allowing your to copy the file itself is that anyone with physical access to your computer can copy the key.

--START HERE --
Here's a summary of how to get it working on debian testing wheezy:

In theory you should install nexus personal from here:
https://install.bankid.com/

I've got v 4.17.0.11 installed on a 64 bit system. The message on this page is a load of bollocks:

Whatever -- the good guys over at Arch supply a link:
wget http://install.bankid.com/Repository/BISP-4.19.0.11351.tar.gz

EDIT: you can use this generic url instead https://install.bankid.com/Download?defaultFileId=Linux

tar -xvf BISP-4.19.0.11351.tar.gz
cd BISP-4.19.0.11351
sudo sh install.4.19.0.11351.sh i

Installing BankID Security Application
ln: failed to create symbolic link `/usr/lib/firefox-addons/plugins': No such file or directory
WARNING: Failed installing plugin for Firefox 3. Manually add symlink to libplugins.so in your Firefox 3 plugin directory if this browser is to be used.
Installation complete.

Since the plugin is 32 bit, you need to link it with nspluginwrapper, and you need 32 bit libs, so

sudo apt-get install nspluginwrapper ia32-libs

Also, as far as I can tell, you need iceweasel/firefox. Chrome/ium won't work.

sudo nspluginwrapper -i /usr/local/lib/personal/libplugins.so

Check to see if it's installed:
nspluginwrapper -l

/usr/lib/mozilla/plugins/npwrapper.libplugins.so
Original plugin: /usr/local/lib/personal/libplugins.so
Plugin viewer: /usr/lib/nspluginwrapper/i386/linux/npviewer
Wrapper version string: 1.3.0

And visit the following page to make sure
https://test.bankid.com/
Or your bank.

Your key -- on a computer where you've used bankid before -- will be in ~/.personal -- don't bother trying to import or export it using the bankid/nexus personal programme (http://popqvarnstrom.blogspot.com.au/2011/06/bankid-nexus-personal-on-ubuntu-1104-64.html) since you're apparently only allowed to do that a certain number of times.

If you just plain copy the files, however, you can do it as many times as you want. I told you the programme is a POS. Anyway,

tree .personal
.personal
|-- backup
|   |-- config
|   |   `-- Personal.cfg
|   `-- store
|-- config
|   `-- Personal.cfg
`-- store
    |-- 1.ngp
    `-- 2.ngp

Nexus Personal/BankID is installed in /usr/local/lib/personal/

Links to this page:
http://popqvarnstrom.blogspot.se/2011/06/bankid-nexus-personal-on-ubuntu-1104-64.html

lindqvist

Anyone who has needs to interact electronically with banks and government agencies in Sweden will become a victim of BankID/Nexus Personal.

It's a piece of crap. I've used it for several years, and have managed to get by. Now, however, if you try to download a newer version (I currently have 4.17.0.11) from a 64 bit debian machine you end up on a page that says:

And there's little hope of getting past it.

Luckily, there's apparently an open-source project, fribid, which may be able to replace bankid/nexus personal for those who don't want to get stuck with 32 bit linux (seriously -- why does 4.17 work on 64 bit and future versions won't? And why won't you let me download an older, supported version? And why can't I chose what version I download? 32 bit windows from a 64 bit linux box -- and vice versa -- SHOULD BE POSSIBLE)

Anyway, fribid:

wget http://fribid.se/releases/source/fribid-1.0.0.tar.bz2
tar -xvf fribid-1.0.0.tar.bz2
cd fribid-1.0.0
./configure
make
sudo make install

I didn't have to do anything to 'install' it beyond that. Navigating in iceweasel to a website requiring bankid started fribid as it should and prompted me for the key file.

I can't explore the functionality beyond this, as fribid can only read keys downloaded with bankid/nexus v 4.10 or earlier -- pk12. The clincher here is that you can download the keys using fribid to begin with instead of first downloading them with bankid.

Lock-in, anyone?

Error:

ERROR: Unsatisfied dependencies:
gtk+-2.0 >= 2.12
gdk-2.0
glib-2.0

Solution:
sudo apt-get install libgtk2.0-dev

lindqvist

UPDATE 16 May 2013: See here for Wine 1.5.30: http://verahill.blogspot.com.au/2013/05/416-wine-1530-in-chroot.html

A more exhaustive description of installing wine in general is here: http://verahill.blogspot.com.au/2012/01/debian-testingwheezy-64-bit-installing.html

I'm not a fan of running windows programmes on linux -- there are enough high-quality packages out there for linux to last you a life-time, and no matter how good wine is¸ the experience of running a windows program on linux is likely to be worse (if faster) than running it natively.

But like most people I'm help prisoner by my fellow co-workers who insists on dog+world using MS Office etc. Also, in spite of everything there are a few pieces of specialised software which lack linux equivalents.

UPDATE (10th Jan 2013): See here for Wine 1.5.21 using the multiarch approach: http://verahill.blogspot.com.au/2013/01/308-compiling-wine-1521-on-debian.html

Finally, from the point of view of easing new users off of windows and onto a real OS, wine and virtualbox fill important functions. I was myself a heavy user of both in the beginning, before learning how to use gnuplot, latex etc.

JPEG support is a PITA, but possible -- see below.

opencl -dev and lib32opencl1 require the contrib non-free repos, e.g.

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

Updated: I've tried the same guide on wine 1.4-rc5

--- START HERE ---
With that out of the way, here's building wine 1.4-rc4

First, you need a whole lot of packages -- these will be installed if you've previously compiled wine according to this:

sudo apt-get install bison flex gcc libc6-dev libfontconfig-dev libfreetype6-dev libglu-dev libgsm1-dev libice-dev libjpeg-dev libldap-dev libmpg123-dev libncurses5-dev libopenal-dev libpng-dev libsm-dev libssl-dev libusb-dev libx11-dev libxcomposite-dev libxcursor-dev libxext-dev libxi-dev libxinerama-dev libxml2-dev libxrandr-dev libxrender-dev libxslt-dev libxt-dev libxxf86vm-dev make libcapi20-dev liblcms-dev libsane-dev libhal-dev libdbus-1-dev valgrind prelink libcups2-dev opencl-dev lib32opencl1 oss4-dev gettext

sudo apt-get install lib32v4l-dev lib32ncurses5-dev lib32asound2-dev lib32z-dev ia32-libs-dev

To enable jpeg support you are SUPPOSED TO:
First, remove existing symlinks
sudo rm /usr/lib32/libjpeg.so.62 /usr/lib32/libjpeg.so.62.0.0
Then, create new ones
sudo ln -s /usr/lib32/libjpeg.so.8 /usr/lib32/libjpeg.so.62
sudo ln -s /usr/lib32/libjpeg.so.8 /usr/lib32/libjpeg.so.62.0.0

Download the sources and expand:
wget http://prdownloads.sourceforge.net/wine/wine-1.4-rc4.tar.bz2
bzip2 -d wine-1.4-rc4.tar.bz2
tar -xvf wine-1.4-rc4.tar
./configure

If you get errors, see below and here for solutions. Missing libraries are often ok -- it just means certain functionality will be missing. It's up to you what is important. If you followed the instructions above you'll have jpeg support in spite of what configure spits out.

make -j7

as usual 7 is the number of cores +1. If you have a dual core, replace 7 with 3. Parallel building is sometimes much, much faster than just using one core, sometimes not.
If you already have a version of wine installed, this is a good time to uninstall it. Then,

sudo checkinstall

builds a .deb package and installs it. It's useful if you need to uninstall in the future.

The

Copying documentation directory...
./
./VERSION
./AUTHORS
./LICENSE
./README
./ANNOUNCE
./COPYING.LIB

part takes forever. It will finish in about ten minutes or so. If the building of the debian package fails, make sure you set the version number correctly (see errors below).

aptitude show wine-1.4

Package: wine-1.4
New: yes
State: installed
Automatically installed: no
Version: 1.4-rc4-1
Priority: extra
Section: checkinstall
Maintainer: root@beryllium
Uncompressed Size: 129 M
Description: Wine 1.4-rc4

Done.

Updated 02/03/2012:

For Wine1.4-rc5:
wget http://sourceforge.net/projects/wine/files/Source/wine-1.4-rc5.tar.bz2

tar -xvf wine-1.4-rc5.tar.bz2

cd wine-1.4-rc5/

./configure

gstreamer, libgsm, libtiff, libjpeg warnings. You can ignore them.
make
sudo checkinstall

List of errors:

Error:
configure: OpenCL 32-bit development files not found, OpenCL won't be supported.

Solution:
sudo apt-get install lib32opencl1 opencl-dev

Error:
configure: gstreamer-0.10 base plugins 32-bit development files not found, gstreamer support disabled
No solution:
Not the only one with this problem...I don't care enough about video to follow this up any more. Likely, an approach similar to this will work: http://forum.winehq.org/viewtopic.php?t=5797&sid=afde9de83a98b8cb24df2bb3646930b6

Error:
configure: OSS sound system found but too old (OSSv4 needed), OSS won't be supported.

Solution:
sudo apt-get install oss4-dev

Error:
configure: libgsm 32-bit development files not found, gsm 06.10 codec won't be supported.
Solution, maybe:
I don't care too much, but there are solutions if you are desperate enough: http://forum.winehq.org/viewtopic.php?t=5797&sid=afde9de83a98b8cb24df2bb3646930b6

Error:

configure: libtiff 32-bit development files not found, TIFF won't be supported.

No soution:

This comes up on some boxes, but not others. Comparing the installed packages I have no idea why.

aptitude search tiff|grep dev

v libtiff-dev -
i A libtiff4-dev - Tag Image File Format (TIFF) library (old
p libtiff5-dev - Tag Image File Format library (TIFF), deve

ls /usr/lib32/libtiff* -lah

/usr/lib32/libtiff.a

/usr/lib32/libtiff.la

/usr/lib32/libtiff.so -> libtiff.so.4.3.3

/usr/lib32/libtiff.so.4 -> libtiff.so.4.3.3

/usr/lib32/libtiff.so.4.3.3

/usr/lib32/libtiffxx.a

/usr/lib32/libtiffxx.la

/usr/lib32/libtiffxx.so -> libtiffxx.so.0.0.7

Error:

configure: WARNING: gettext tools not found, translations won't be built.
Solution:
sudo apt-get install gettext

Error:
configure: WARNING: libjpeg 32-bit development files not found, JPEG won't be supported.

Solution:
First, install
sudo apt-get install libjpeg8-dev

This pointed me here.

Here's how to check for the bug
locate libjpeg | grep 32

/usr/lib32/libjpeg.a
/usr/lib32/libjpeg.la
/usr/lib32/libjpeg.so
/usr/lib32/libjpeg.so.62
/usr/lib32/libjpeg.so.62.0.0
/usr/lib32/libjpeg.so.8
/usr/lib32/libjpeg.so.8.0.2

ls /usr/lib32/libjpeg.* -lah

/usr/lib32/libjpeg.a

/usr/lib32/libjpeg.la

/usr/lib32/libjpeg.so -> libjpeg.so.62.0.0

/usr/lib32/libjpeg.so.62 -> libjpeg.so.62.0.0

/usr/lib32/libjpeg.so.62.0.0

/usr/lib32/libjpeg.so.8 -> libjpeg.so.8.0.2

/usr/lib32/libjpeg.so.8.0.2

Yup, libjpeg.so points to v 6.2 instead of v 8 which I have installed.

According to the bug report, the cause of the error is that the header file jpeglib.h states one version, and the /usr/lib32/libjpeg.so points to another:

cat /usr/include/jpeglib.h|grep "LIB_VERSION"| grep define

#define JPEG_LIB_VERSION 80 /* Compatibility version 8.0 */
#define JPEG_LIB_VERSION_MAJOR 8
#define JPEG_LIB_VERSION_MINOR 4

FIX:

Remove existing symlinks

sudo rm /usr/lib32/libjpeg.so.62 /usr/lib32/libjpeg.so.62.0.0

Create new ones

sudo ln -s /usr/lib32/libjpeg.so.8 /usr/lib32/libjpeg.so.62

sudo ln -s /usr/lib32/libjpeg.so.8 /usr/lib32/libjpeg.so.62.0.0

ls /usr/lib32/libjpeg.* -lah now gives

/usr/lib32/libjpeg.a

/usr/lib32/libjpeg.la

/usr/lib32/libjpeg.so -> libjpeg.so.62.0.0

/usr/lib32/libjpeg.so.62 -> /usr/lib32/libjpeg.so.8

/usr/lib32/libjpeg.so.62.0.0 -> /usr/lib32/libjpeg.so.8

/usr/lib32/libjpeg.so.8 -> libjpeg.so.8.0.2

/usr/lib32/libjpeg.so.8.0.2

The error message remains on ./configure, but jpeg support is /supposed/ to work in spite of this.

Error:

Building Debian package... FAILED!
*** Failed to build the package
Do you want to see the log file? [y]:
dpkg-deb: error: parsing file '/var/tmp/tmp.Y50XUaisW0/package/DEBIAN/control' near line 7 package 'wine-1.4': error in Version string 'rc4-1': version number does not start with digit

Solution:

sudo checkinstall

This package will be built according to these values:
0 - Maintainer: [ root@beryllium ]
1 - Summary: [ Wine 1.4-rc4 ]
2 - Name: [ wine-1.4 ]
3 - Version: [ rc4 ]
4 - Release: [ 1 ]
5 - License: [ GPL ]
6 - Group: [ checkinstall ]
7 - Architecture: [ amd64 ]
8 - Source location: [ wine-1.4-rc4 ]
9 - Alternate source location: [ ]
10 - Requires: [ ]
11 - Provides: [ wine-1.4 ]
12 - Conflicts: [ ]
13 - Replaces: [ ]
Enter a number to change any of them or press ENTER to continue: 3
Enter new version:
>> 1.4-rc4

lindqvist

The situation:
you have a DSL service with a dynamic IP. Your IP typically changes once per month or so, perhaps a bit more often. It would be nice to connect a domain name to your IP address and have it automatically point in the right direction.

The solution:
The easiest way to do this is probably by using the tomato router firmware for linksys routers. Presuming that you've got it installed and running:

1. Register for a free dns account at freedns.afraid.org
2. Create a subdomain e.g. jibberjabber.mooo.com. Link it to an IP address.

3. Generate a URL for dynamic update

4. Log on to your router and add the URL (the irrelevant parts will probably be excised automatically)

5. Wait. It will take a couple of hours for the domain name to point in the right direction. In the beginning my domain name pointed at 127.0.0.2.

lindqvist

EDIT 18 May 2012:
It's now been solved
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

UPDATE April 2012: Someone else is having the same problem: http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id435/ . Binaries built on ROCKS 5.4.3 work, but binaries built on debian testing don't: the gfortran version is GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-50). On debian, which yields a segfaulting binary, the version is GNU Fortran (Debian 4.6.3-1) 4.6.3

Nwchem 6.1 was released in February this year. The build instructions are ALMOST the same as for Nwchem 6.0 -- the difference is the use of export USE_MPIF4=y. Well, that and me not having much success in actually USING nwchem as opposed to building it.

There is now an nwchem version with mpi support in the debian unstable repos. I have not used or tested it.

I can build the 32 bit version of nwchem 6.1 just fine.Building the 64 bit version works absolutely fine too. However, once you attempt to run, it crashes. Ergo, this is NOT A SOLUTION. It's a bunch of error messages so that more seasoned and skilled operators than I may offer a solution. If you have an option, build and use version 6.0 instead.

Update:
I built a version with openmpi support as well, which also segfaults:
Here are the build instructions:

sudo apt-get install openmpi-bin openmpi-dev
export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=/home/me/tmp/nwchem-6.1
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export MPI_LOC=/usr/lib/openmpi
export MPI_INCLUDE=/usr/lib/openmpi/include
export USE_MPIF4=y
export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib/openmpi/lib
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran

and here's what happens on execution

[beryllium:24650] *** Process received signal ***
[beryllium:24650] Signal: Segmentation fault (11)
[beryllium:24650] Signal code: Address not mapped (1)
[beryllium:24650] Failing at address: 0x44000098
[beryllium:24650] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x324f0) [0x7f08deeb84f0]
[beryllium:24650] [ 1] /usr/lib/libmpi.so.0(PMPI_Comm_set_errhandler+0x60) [0x7f08e0526c30]
[beryllium:24650] [ 2] ./nwchem() [0x292d504]
[beryllium:24650] [ 3] ./nwchem() [0x292d596]
[beryllium:24650] [ 4] ./nwchem() [0x40657a]
[beryllium:24650] [ 5] ./nwchem() [0x406f7d]
[beryllium:24650] [ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd) [0x7f08deea4ead]
[beryllium:24650] [ 7] ./nwchem() [0x405189]
[beryllium:24650] *** End of error message ***

This only happens on 64 bit debian -- 32 bit deb and 64 bit centos are both fine

OLD POST:

--start here --

Here's what I've done so far

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

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-10.tar.gz
cd nwchem-6.1

create buildconf.sh in ~/nwchem-6.1
Put the following in it (for 64 bit system):

export LARGE_FILES=TRUE
export TCGRSH=/usr/local/bin/ssh
export NWCHEM_TOP=/home/me/nwchem-6.1
export NWCHEM_TARGET=LINUX64
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"
export NWCHEM_MODULES="all"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran

Build
Start the build
sh buildconf.sh

Building takes about half an hour. Everything builds fine. However, running -- with or without mpdrun -- causes the error below.

It doesn't matter how much memory I allocated. The error seems to have something to do with "Invalid write of size 8" which I understand to mean that pointers are 8 bytes long but don't have 8 bytes allocated to them. But then I'm not an expert.

Would it have something to do with
USE_MPIF4=y?

Without USE_MPIF4 I end up with the stupid_* error messages (stupid_sum, stupid_task etc.)

Error:
running e.g. mpdrun -n 2 nwchem nwchem.nw gives:

Screening Tolerance Information
-------------------------------
Density screening/tol_rho: 1.00D-10
AO Gaussian exp screening on grid/accAOfunc: 14
CD Gaussian exp screening on grid/accCDfunc: 20
XC Gaussian exp screening on grid/accXCfunc: 20
Schwarz screening/accCoul: 1.00D-08

0:Segmentation Violation error, status=: 11
(rank:0 hostname:tantalum pid:19944):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0

More detail:
Running just nwchem nwchem.nw gives a bit more detail:

Screening Tolerance Information
-------------------------------
Density screening/tol_rho: 1.00D-10
AO Gaussian exp screening on grid/accAOfunc: 14
CD Gaussian exp screening on grid/accCDfunc: 20
XC Gaussian exp screening on grid/accXCfunc: 20
Schwarz screening/accCoul: 1.00D-08

0:Segmentation Violation error, status=: 11
(rank:0 hostname:tantalum pid:19676):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
application called MPI_Abort(comm=0x84000001, 11) - process 0
*** glibc detected *** nwchem: corrupted double-linked list: 0x000000010ac34880 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x75ab6)[0x7f597b129ab6]
/lib/x86_64-linux-gnu/libc.so.6(+0x7754c)[0x7f597b12b54c]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c)[0x7f597b12e7ec]
/usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0xcc811)[0x7f597bbd5811]
/usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0xdba7f)[0x7f597bbe4a7f]
/usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0xdbbaa)[0x7f597bbe4baa]
/usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0x1ab09)[0x7f597bb23b09]
/lib64/ld-linux-x86-64.so.2(+0xe21c)[0x7f597c42421c]
/lib/x86_64-linux-gnu/libc.so.6(+0x36df2)[0x7f597b0eadf2]
/lib/x86_64-linux-gnu/libc.so.6(+0x36e45)[0x7f597b0eae45]
/usr/lib/libmpich.so.1.2(+0xbedc9)[0x7f597c101dc9]
/usr/lib/libmpich.so.1.2(MPID_Abort+0x6d)[0x7f597c122d0d]
/usr/lib/libmpich.so.1.2(PMPI_Abort+0x2f5)[0x7f597c090805]
nwchem[0x2896591]
nwchem[0x2883883]
/lib/x86_64-linux-gnu/libc.so.6(+0x324f0)[0x7f597b0e64f0]
nwchem[0x29b6043]
nwchem[0x27a04a0]
nwchem[0x27a3955]
nwchem[0x271492b]
nwchem[0x5cf410]
nwchem[0x5b3d18]
nwchem[0x5a9735]
nwchem[0x5a99b6]
nwchem[0x418ee8]
nwchemAborted

And more detail:

valgrind nwchem nwchem.nw

==19910== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==19910== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==19910== by 0x5A9734: nwdft_ (nwdft.F:274)
==19910== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==19910== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==19910== by 0x41A57B: task_energy_ (task_energy.F:95)
==19910== by 0x40DAD2: task_ (task.F:337)
==19910== by 0x4068F5: MAIN__ (nwchem.F:251)
==19910== Address 0x199750a0 is not stack'd, malloc'd or (recently) free'd
==19910==
==19910== Invalid write of size 8
==19910== at 0x29B6043: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==19910== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==19910== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==19910== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==19910== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==19910== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==19910== by 0x5A9734: nwdft_ (nwdft.F:274)
==19910== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==19910== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==19910== by 0x41A57B: task_energy_ (task_energy.F:95)
==19910== by 0x40DAD2: task_ (task.F:337)
==19910== by 0x4068F5: MAIN__ (nwchem.F:251)
==19910== Address 0x199750b0 is not stack'd, malloc'd or (recently) free'd
==19910==
0:Segmentation Violation error, status=: 11
(rank:0 hostname:tantalum pid:19910):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
application called MPI_Abort(comm=0x84000001, 11) - process 0
==19910==
==19910== HEAP SUMMARY:
==19910== in use at exit: 4,303,284,335 bytes in 695 blocks
==19910== total heap usage: 2,132 allocs, 1,437 frees, 4,305,897,103 bytes allocated
==19910==
==19910== LEAK SUMMARY:
==19910== definitely lost: 24 bytes in 1 blocks
==19910== indirectly lost: 512 bytes in 1 blocks
==19910== possibly lost: 0 bytes in 0 blocks
==19910== still reachable: 4,303,283,799 bytes in 693 blocks
==19910== suppressed: 0 bytes in 0 blocks
==19910== Rerun with --leak-check=full to see details of leaked memory
==19910==
==19910== For counts of detected and suppressed errors, rerun with: -v
==19910== Use --track-origins=yes to see where uninitialised values come from
==19910== ERROR SUMMARY: 662 errors from 9 contexts (suppressed: 4 from 4)

And way too much detail:
valgrind --leak-check=full --track-origins=yes --log-file=valgrind.log nwchem nwchem.nw
==20005== Memcheck, a memory error detector

==20005== Memcheck, a memory error detector
==20005== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
==20005== Using Valgrind-3.6.1 and LibVEX; rerun with -h for copyright info
==20005== Command: nwchem nwchem.nw
==20005== Parent PID: 19563
==20005==
==20005== Warning: set address range perms: large range [0x3952b040, 0x13352b110) (undefined)
==20005== Syscall param write(buf) points to uninitialised byte(s)
==20005== at 0x12803980: __write_nocancel (syscall-template.S:82)
==20005== by 0x127A8B92: _IO_file_write@@GLIBC_2.2.5 (fileops.c:1276)
==20005== by 0x127A8809: new_do_write (fileops.c:530)
==20005== by 0x127A8B34: _IO_do_write@@GLIBC_2.2.5 (fileops.c:503)
==20005== by 0x127A9347: _IO_file_sync@@GLIBC_2.2.5 (fileops.c:905)
==20005== by 0x1279DE19: fflush (iofflush.c:43)
==20005== by 0xA3CF1F: hdbm_file_flush (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x8C84AA: rtdb_seq_put (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x8C55BD: rtdb_put (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x8C48B2: rtdb_put_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x9EAFAC: util_set_rtdb_state_ (util_rtdb_state.F:40)
==20005== by 0x4067FD: MAIN__ (nwchem.F:222)
==20005== Address 0x10950022 is not stack'd, malloc'd or (recently) free'd
==20005== Uninitialised value was created by a stack allocation
==20005== at 0x8C6130: rtdb_seq_put_info (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B6048: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x19975040 is 0 bytes after a block of size 42,008,576 alloc'd
==20005== at 0x1155679D: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==20005== by 0x291F69B: morecore (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x291F793: kr_malloc (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A492B: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B604D: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x19975050 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B6052: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x19975060 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B6057: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x19975070 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B6035: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x19975080 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B6039: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x19975090 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B603E: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x199750a0 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005== Invalid write of size 8
==20005== at 0x29B6043: dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A049F: GAI_DGEMM (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x27A3954: pnga_matmul (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x271492A: ga_dgemm_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5CF40F: diis_bld12_ (in /home/me/nwchem-6.1/bin/LINUX64/nwchem)
==20005== by 0x5B3D17: dft_main0d_ (dft_main0d.F:549)
==20005== by 0x5A9734: nwdft_ (nwdft.F:274)
==20005== by 0x5A99B5: dft_energy_ (nwdft.F:18)
==20005== by 0x418EE7: task_energy_doit_ (task_energy.F:251)
==20005== by 0x41A57B: task_energy_ (task_energy.F:95)
==20005== by 0x40DAD2: task_ (task.F:337)
==20005== by 0x4068F5: MAIN__ (nwchem.F:251)
==20005== Address 0x199750b0 is not stack'd, malloc'd or (recently) free'd
==20005==
==20005==
==20005== HEAP SUMMARY:
==20005== in use at exit: 4,303,284,355 bytes in 697 blocks
==20005== total heap usage: 2,135 allocs, 1,438 frees, 4,305,900,787 bytes allocated
==20005==
==20005== 536 (24 direct, 512 indirect) bytes in 1 blocks are definitely lost in loss record 662 of 679
==20005== at 0x1155679D: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==20005== by 0x11D6E128: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==20005== by 0x11E332F8: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==20005== by 0x11E2C573: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==20005== by 0x11D6BB47: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==20005== by 0x1093CCCF: call_init (dl-init.c:85)
==20005== by 0x1093CDC6: _dl_init (dl-init.c:134)
==20005== by 0x1092FB29: ??? (in /lib/x86_64-linux-gnu/ld-2.13.so)
==20005== by 0x1: ???
==20005== by 0x7FF00033A: ???
==20005== by 0x7FF000341: ???
==20005==
==20005== LEAK SUMMARY:
==20005== definitely lost: 24 bytes in 1 blocks
==20005== indirectly lost: 512 bytes in 1 blocks
==20005== possibly lost: 0 bytes in 0 blocks
==20005== still reachable: 4,303,283,819 bytes in 695 blocks
==20005== suppressed: 0 bytes in 0 blocks
==20005== Reachable blocks (those to which a pointer was found) are not shown.
==20005== To see them, rerun with: --leak-check=full --show-reachable=yes
==20005==
==20005== For counts of detected and suppressed errors, rerun with: -v
==20005== ERROR SUMMARY: 663 errors from 10 contexts (suppressed: 4 from 4)

For comparison, here's using nwchem 6.0:
NOTE that this version works just fine and runs to completion without error messages normally.
valgrind --leak-check=full --track-origins=yes --log-file=valgrind.log nwchem nwchem.nw

==21014== Memcheck, a memory error detector
==21014== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
==21014== Using Valgrind-3.6.1 and LibVEX; rerun with -h for copyright info
==21014== Command: nwchem nwchem.nw
==21014== Parent PID: 20854
==21014==
==21014== Warning: set address range perms: large range [0x3952b040, 0x13352b110) (undefined)
==21014== Syscall param write(buf) points to uninitialised byte(s)
==21014== at 0x11673980: __write_nocancel (syscall-template.S:82)
==21014== by 0x11618B92: _IO_file_write@@GLIBC_2.2.5 (fileops.c:1276)
==21014== by 0x11618809: new_do_write (fileops.c:530)
==21014== by 0x11618B34: _IO_do_write@@GLIBC_2.2.5 (fileops.c:503)
==21014== by 0x11619347: _IO_file_sync@@GLIBC_2.2.5 (fileops.c:905)
==21014== by 0x1160DE19: fflush (iofflush.c:43)
==21014== by 0x8A16D7: hdbm_file_flush (in /home/me/nwchem-6.0/bin/LINUX64/nwchem)
==21014== by 0x83C973: rtdb_seq_put (in /home/me/nwchem-6.0/bin/LINUX64/nwchem)
==21014== by 0x83ADA6: rtdb_put (in /home/me/nwchem-6.0/bin/LINUX64/nwchem)
==21014== by 0x83A13F: rtdb_put_ (in /home/me/nwchem-6.0/bin/LINUX64/nwchem)
==21014== by 0x85C72C: util_set_rtdb_state_ (util_rtdb_state.F:40)
==21014== by 0x40636B: MAIN__ (nwchem.F:223)
==21014== Address 0xf7c0022 is not stack'd, malloc'd or (recently) free'd
==21014== Uninitialised value was created by a stack allocation
==21014== at 0x83B7D0: rtdb_seq_put_info (in /home/me/nwchem-6.0/bin/LINUX64/nwchem)
==21014==
==21014== Conditional jump or move depends on uninitialised value(s)
==21014== at 0x8A5E1F: sym_op_class_name_ (sym_op_cname.F:26)
==21014== by 0x83FB41: sym_op_classify_ (sym_op_clsfy.F:49)
==21014== by 0x845AE9: sym_movecs_adapt_ (sym_mo_adapt.F:77)
==21014== by 0x719A4A: scf_movecs_sym_adapt_ (scf_sym_adap.F:70)
==21014== by 0x731028: scf_vectors_guess_ (scf_vec_guess.F:403)
==21014== by 0x58D4E6: dft_scf_ (dft_scf.F:526)
==21014== by 0x58B67B: dft_main0d_ (dft_main0d.F:537)
==21014== by 0x5818B3: nwdft_ (nwdft.F:309)
==21014== by 0x581B24: dft_energy_ (nwdft.F:18)
==21014== by 0x4174D7: task_energy_doit_ (task_energy.F:229)
==21014== by 0x418AEB: task_energy_ (task_energy.F:74)
==21014== by 0x40C646: task_ (task.F:301)
==21014== Uninitialised value was created by a stack allocation
==21014== at 0x83F9BD: sym_op_classify_ (sym_op_clsfy.F:32)
==21014==
==21014==
==21014== HEAP SUMMARY:
==21014== in use at exit: 4,254,665,672 bytes in 20 blocks
==21014== total heap usage: 10,491 allocs, 10,471 frees, 4,275,242,731 bytes allocated
==21014==
==21014== 17 bytes in 2 blocks are definitely lost in loss record 9 of 19
==21014== at 0x103C679D: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==21014== by 0x11626881: strdup (strdup.c:43)
==21014== by 0x24D33F7: pbeginf_ (in /home/me/nwchem-6.0/bin/LINUX64/nwchem)
==21014== by 0x405F53: MAIN__ (nwchem.F:66)
==21014== by 0x406964: main (nwchem.F:336)
==21014==
==21014== 536 (24 direct, 512 indirect) bytes in 1 blocks are definitely lost in loss record 13 of 19
==21014== at 0x103C679D: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==21014== by 0x10BDE128: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==21014== by 0x10CA32F8: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==21014== by 0x10C9C573: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==21014== by 0x10BDBB47: ??? (in /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0)
==21014== by 0xF7ACCCF: call_init (dl-init.c:85)
==21014== by 0xF7ACDC6: _dl_init (dl-init.c:134)
==21014== by 0xF79FB29: ??? (in /lib/x86_64-linux-gnu/ld-2.13.so)
==21014== by 0x1: ???
==21014== by 0x7FF00032A: ???
==21014== by 0x7FF000331: ???
==21014==
==21014== LEAK SUMMARY:
==21014== definitely lost: 41 bytes in 3 blocks
==21014== indirectly lost: 512 bytes in 1 blocks
==21014== possibly lost: 0 bytes in 0 blocks
==21014== still reachable: 4,254,665,119 bytes in 16 blocks
==21014== suppressed: 0 bytes in 0 blocks
==21014== Reachable blocks (those to which a pointer was found) are not shown.
==21014== To see them, rerun with: --leak-check=full --show-reachable=yes
==21014==
==21014== For counts of detected and suppressed errors, rerun with: -v
==21014== ERROR SUMMARY: 178 errors from 4 contexts (suppressed: 4 from 4)

lindqvist

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.

lindqvist

Follows this with minor amendments.

The issue:
You start e.g. a compile or a number-crunching job on your work computer, and go home while leaving it running. When you get home you log on to your work computer via ssh, and want to connect to the terminal in which the job is running i.e. connect to the tty.

Another use for screen is if you are working over an unstable connection -- if you get booted off the screen session continues to run, so whatever was running in it is still sound. A normal pts will die and crash.

A solution using screen:
Be aware that this can cause a potential security risk.

1. install gnu screen
sudo apt-get install screen

2. enable multi-user mode
sudo chmod +s /usr/bin/screen
sudo chmod 755 /var/run/screen

Edit /etc/screenrc and add the following lines anywhere

multiuser on
acladd me

If you want primitive scrolling (shift + page up/down)

termcapinfo xterm|xterms|xs|rxvt ti@:te@

Replace me with the local username.

3. On your work computer,
screen -S testing

4. Start whatever job you were thinking of and leave it running

5. From home ssh into your work computer then
screen -x me/testing

Another neat thing is that both terminals look the same no matter whether you are at your work computer or at your home computer. Ergo, it may be a useful way of helping people remotely with their computers too.

6. To disconnect gracefully
Hold CTRL+a+d

Do not type exit or anything like that, as it will close the screen instance completely.

For a gnu screen cheat sheet, look here:
http://www.totiso.com/2009/05/03/gnu-screen-cheat-sheet

lindqvist

The version of maxima in the debian repos is the same as in the sourceforge archives. There's only one good reason to compile your own version from what I can see -- to get around the dependency of maxima on gnuplot.

Let me explain: the gnuplot version in the debian repos has problems handling small numbers (<10**(-9)). Uninstalling gnuplot and replacing it with your a version you've compiled yourself removes maxima.

Luckily it's easy to build:

wget http://sourceforge.net/projects/maxima/files/latest/download?source=files

mv download\?source\=files maxima-5.26.0.tar.gz

./configure

make -j5

where 5 is the number of cores +1 (I have four cores). Change as needed.

sudo checkinstall

Checkinstall may or may not exit successfully if you have compiled your own version of gnuplot -- see below. Chances are that it built the package correctly.

or

sudo make install

Error:

If you get

dpkg: error processing maxima_5.26.0-1_amd64.deb (--install):
trying to overwrite '/usr/local/share/info/dir', which is also in package gnuplot 4.4.4-1
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)

Solution:

sudo dpkg --force-overwrite -i maxima_5.26.0-1_amd64.deb

You can see that the dir file is ok (GNUPlot is still referred to):

This is the file .../info/dir, which contains the
topmost node of the Info hierarchy, called (dir)Top.
The first time you invoke Info you start off looking at this node.

File: dir, Node: Top This is the top of the INFO tree
This (the Directory node) gives a menu of major topics.
Typing "q" exits, "?" lists all Info commands, "d" returns here,
"h" gives a primer for first-timers,
"mEmacs<Return>" visits the Emacs manual, etc.
In Emacs, you can click mouse button 2 on a menu item or cross reference
to select it.
* Menu:
Emacs
* Imaxima: (imaxima). Image support for the computer algebra system
Maxima. Interactive math minor mode.
Math
* GNUPLOT: (gnuplot). An Interactive Plotting Program
* Maxima: (maxima). A computer algebra system.
* Xmaxima: (xmaxima). Graphical interface for Maxima.

lindqvist

I use evolution for email, contacts and calendar because it integrates well with gnome and because it looks a whole lot prettier than the version of Thunderbird (i.e. Icedove) in the debian repos (3.1.16-1).

Well, sometimes you've got to check out the alternatives. Here's how to build thunderbird 10.0.2 from source.

-- START HERE --

sudo apt-get install libdbus-glib-1-dev gir1.2-notify-0.7 libnotify-dev yasm checkinstall libzip-dev zip

cd ~/tmp
wget ftp://ftp.mozilla.org/pub/mozilla.org/thunderbird/releases/10.0.2/source/thunderbird-10.0.2.source.tar.bz2

tar -xvf thunderbird-10.0.2.source.tar.bz2

cd comm-release/

./configure --disable-necko-wifi

..
updating cache ../../.././config.cache
creating ./config.status
creating Makefile
creating config/Makefile
creating config/autoconf.mk
creating ldap/Makefile
creating ldap/clients/tools/Makefile
creating ldap/include/Makefile
creating ldap/libraries/Makefile
creating ldap/libraries/libldap/Makefile
creating ldap/libraries/libprldap/Makefile
creating ldap/libraries/libldif/Makefile
creating ldap/libraries/liblber/Makefile
creating ldap/libraries/libiutil/Makefile
creating ldap/libraries/libssldap/Makefile
creating ldap/libraries/libutil/Makefile

make -jN

...
make[4]: Leaving directory `/home/me/tmp/comm-release/mail/test/mozmill'
make[3]: Leaving directory `/home/me/tmp/comm-release/mail'
make[2]: Leaving directory `/home/me/tmp/comm-release'
make[1]: Leaving directory `/home/me/tmp/comm-release'
if test -d ./mozilla/dist/bin ; then touch ./mozilla/dist/bin/.purgecaches ; fi

where N is the number of cores +1 -- in my case it's 7 since I have a six-core CPU. Be aware that building does take a while.

sudo make install

(sudo checkinstall ended with segfault for some reason)

You are now done.

Make sure that /usr/local/bin is in your PATH

me@beryllium:~/tmp/comm-release$ which thunderbird
/usr/local/bin/thunderbird

Interesting observation:
while thunderbird starts thunderbird the home-built version seems to be referred to as earlybird:

What's ugly or not is subjective, but you may want to use this add-on:
https://addons.mozilla.org/en-US/thunderbird/addon/gnome-linux-integration/?src=search

Troubleshooting:
Error:
checking MOZ_PANGO_CFLAGS... -pthread -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/freetype2
checking MOZ_PANGO_LIBS... -pthread -lpangoft2-1.0 -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0
checking for gnome-vfs-2.0 >= 2.0 gnome-vfs-module-2.0 >= 2.0... checking for gconf-2.0 >= 1.2.1 gobject-2.0 ... checking for dbus-glib-1 >= 0.60... Package dbus-glib-1 was not found in the pkg-config search path. Perhaps you should add the directory containing `dbus-glib-1.pc' to the PKG_CONFIG_PATH environment variable No package 'dbus-glib-1' found
configure: error: Library requirements (dbus-glib-1 >= 0.60) not met; consider adjusting the PKG_CONFIG_PATH environment variable if your libraries are in a nonstandard prefix so pkg-config can find them.

Solution:
sudo apt-get install libdbus-glib-1-dev

Error:

checking MOZ_PANGO_LIBS... -pthread -lpangoft2-1.0 -lfreetype -lfontconfig -lpangocairo-1.0 -lpango-1.0 -lcairo -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0
checking for gnome-vfs-2.0 >= 2.0 gnome-vfs-module-2.0 >= 2.0... checking for gconf-2.0 >= 1.2.1 gobject-2.0 ... checking for libnotify >= 0.4... Package libnotify was not found in the pkg-config search path. Perhaps you should add the directory containing `libnotify.pc' to the PKG_CONFIG_PATH environment variable No package 'libnotify' found
configure: error: Library requirements (libnotify >= 0.4) not met; consider adjusting the PKG_CONFIG_PATH environment variable if your libraries are in a nonstandard prefix so pkg-config can find them

Solution:
sudo apt-get install gir1.2-notify-0.7 libnotify-dev

Error:

checking MOZ_DBUS_GLIB_LIBS... -pthread -ldbus-glib-1 -ldbus-1 -lpthread -lgobject-2.0 -lgthread-2.0 -lrt -lglib-2.0
checking __attribute__ ((aligned ())) support... trying 64
64
configure: error: yasm is a required build tool for this architecture when webm is enabled. You may either install yasm or --disable-webm (which disables the WebM video format). See https://developer.mozilla.org/en/YASM for more details.
configure: error: ./configure failed for mozilla

Solution:
sudo apt-get install yasm

lindqvist

Update 17 March 2013: See this post for a faster, better way of creating a full install if you're already running Debian.

Original post:
Every now and again I get posts like this one, or this one, via google news. While those posts --describing the use of unetbootin to create a 'live' USB analogue to a live CD -- may be technically correct, there's just so much more you can do.

In 1 we do the old boring bog-standard 'write live cd to a usb' thingy that you see pasted all over the web, but using cat instead of unetbootin.
In 2 we make a real, bootable installation on a usb drive.

1. Creating a USB version of a live CD -- the boring option
With the current 'hybrid' Debian iso's it couldn't be easier.
THIS WILL WIPE YOUR USB STICK

--- START HERE ---

a. Download the iso
Using jigdo is a good option. Downloading a business-card/netinstall iso is another, if you'll have a working internet connection available.

b. Plug in and mount your USB device and find out the device name of your USB drive.
If it's mounted you can use
df -h

rootfs 93G 36G 54G 40% /
udev 3.9G 0 3.9G 0% /dev
tmpfs 801M 980K 800M 1% /run
/dev/disk/by-uuid/..-10a350f85687 93G 36G 54G 40% /
tmpfs 5.0M 0 5.0M 0% /run/lock
tmpfs 1.6G 52K 1.6G 1% /tmp
tmpfs 1.6G 816K 1.6G 1% /run/shm
/dev/sda6 745G 183G 525G 26% /home
/dev/sdc1 2.0G 434M 1.5G 23% /media/XP-KOMKU

or

mount

../dev/sdc1 on /media/XP-KOMKU type vfat (rw,nosuid,nodev,relatime,uid=1000,gid=1000,fmask=0022,dmask=0077,codepage=cp437,iocharset=utf8,shortname=mixed,showexec,utf8,flush,errors=remount-ro,uhelper=udisks)

to list mounted devices. In my case it's an old 2 G usb stick I used to create a Windows XP installation USB device on.

If you prefer a gui tool, start palimpsest (called Disk Utility in gnome)
It will be something akin to sdb1 or sdc1 etc. That means the device name is /dev/sdb or /dev/sdc, respectively. In our case, it's sdc.

c. Unmount but don't detach the device
You don't want anything else writing to it.

me@beryllium:~/Documents/screengrabs$ umount /dev/sdc1
me@beryllium:~/Documents/screengrabs$ df -h
Filesystem Size Used Avail Use% Mounted on
rootfs 93G 36G 54G 40% /
udev 3.9G 0 3.9G 0% /dev
tmpfs 801M 976K 800M 1% /run
/dev/disk/by-uuid/..-10a350f85687 93G 36G 54G 40% /
tmpfs 5.0M 0 5.0M 0% /run/lock
tmpfs 1.6G 60K 1.6G 1% /tmp
tmpfs 1.6G 820K 1.6G 1% /run/shm
/dev/sda6 745G 183G 525G 26% /home

d. Become root and use cat to write the iso to the USB device

sudo su

And write (assuming that the device name is sdc and you are using the businesscard iso)

cat debian-6.0.3-amd64-businesscard.iso > /dev/sdc

Done.

e. boot from your USB drive and go through the same steps as for a CD.
Plug it in, then start your computer. Hit F12 (or F10 or del or F2) during the bios start-up to select boot medium. Choose to boot from usb. Older BIOSes can't boot from USB.

2. Really INSTALLING Debian on a USB
You can use either virtualbox or quemu for this. Here I show how to use virtualbox.

[NOTE: there's a leaner, faster, better way described here: http://verahill.blogspot.com/2013/03/361-installing-debian-on-usb-stick-from.html ]

Note that a tiny 2 Gb USB stick isn't suitable for a full Debian + Gnome installation. It may, however, work well with e.g. openbox and xmonad. Or just work in the terminal -- use mutt for email, mcabber for chat, elinks for http/www etc.
Here I show how to install using the businesscard iso, but I've done this with the regular Debian DVD version in the past.
Also, few USB devices operate at 480 Mbps -- so be prepared that installation via virtualbox onto a USB device will take considerably longer than a regular installation.
Solid state devices degrade with I/O, so use your USB stick for back-up use during e.g. travel etc. Don't trust the integrity of it.

There are a few good reasons for installing a full linux version on a thumb drive or a regular but external harddrive:
* a thumb drive will allow you too carry an independent OS with you, allowing you to e.g. temporarily borrow a computer from a friend but running your own system. An installation, as opposed to a 'live cd', allows you to customise the setup and install programs. USB 2 is quite slow, and many thumb drives are slower than that, so you're probably better off running a light system than a full on gnome-shell desktop. That's not so say that you can't -- I have.
* installing onto a usb-connected harddrive will allow you to setup and prepare headless boxes or systems without a direct internet connection.

First you need to install virtualbox, which is available in the debian repos (sudo apt-get install virtualbox virtualbox-guest-additions), and -- in order to enable USB 2 support -- the "VirtualBox 4.1.8 Oracle VM VirtualBox Extension Pack" from https://www.virtualbox.org/wiki/Downloads
Start virtualbox and go to File/Preferences/Extensions to install the extension pack you downloaded.

--- START HERE ---

Installing debian (or any os) on an external USB stick/drive using virtualbox
a. Start virtualbox and click on New.

b. Click through the Name, Operating System and Version questions, Select a memory size which is reasonable for the intended use and target machine. Give it at least 256 Mb. Don't fret about this step -- on each boot your system will autodetect the amount of available RAM. The next question is the key to the whole undertaking: DO NOT SET A START-UP DISK (or any virtual harddisk)

In the next dialogue box you'll be asked if you want to continue or go back - yes, you want to continue.

c. Your new machine is now ready to be set up. Select it and click on settings; Got to storage, IDE controller and choose a virtual CD/DVD disk file. Select the debian installation iso.

d. Next click on USB, enable USB 2 controller, and add a filter for your device by e.g. hitting alt+insert and selecting it from the list.

e. You're ready to install! Start the virtual machine, and the installation should start without you having to select boot device. Most of the setting are the same as in any normal install. Pay attention when you come to the Partition Disk dialogue though. Make sure that you're not doing something silly and accidentally deleting something you shouldn't be a-deleting, even though the risks of that are very slim.

Delete the existing partitions and create a new one. I added a tiny swap space too, hoping that this will make the difference between a freeze and a slow crawl on underpowered systems.

f. Continue with the installation as normal.

g. Postscript:
* /dev/sda1 vs UUID. Once you're done with the installation and have shut down your virtualbox, mount the USB drive as a normal thumb drive and have a look at fstab in particular -- if you're using relative paths (e.g. sda) instead of absolute paths using UUID, you may run into problems at some point.

In the screengrab you see that

# / was on /dev/sda1 during installation

UUID=8c0c9c98-e73f-4f5a-b7d7-f91f95c9d8ca / ext4 errors=remount-ro 0 1

Which means we're good.

You may want to comment out

/dev/sda1 /media/usb0 auto rw,user,noauto 0 0
/dev/sda2 /media/usb1 auto rw,user,noauto 0 0
/dev/sda5 /media/usb2 auto rw,user,noauto 0 0

But I haven't in the past and all has been good.

* network interfaces -- you may find that no network interface is configured for you and that no interface shows up when you use ifconfig. Use ip addr to get a list over interfaces. If the interface is e.g. eth2, you may want to edit /etc/network/interfaces and add

auto eth2
iface eth2 inet dhcp

or (the ip's are just examples)

auto eth2
iface eth2 inet static
address 192.168.1.100
gateway 192.168.1.1
netmask 255.255.255.0

And then run sudo service networking restart

That's it. You now have a full installation on either a 'removable' drive or on an HDD which you can install in a desktop/laptop.

Links to this page:
http://vk.com/topic-50603_27808581
http://forum.debian.org.tr/arsiv-konu-391.0-debian-live-usb.html
http://alsamixer.wordpress.com/2012/10/07/installing-debian/
http://cv.uoc.edu/app/phpBB3/viewtopic.php?f=3511&t=20897
http://www.computerbase.de/forum/showthread.php?t=1208228&p=13936928

Pages

26 February 2012

79. Bankid/nexus personal and iceweasel on Debian Testing

78. Fribid as an alternative to nexus personal on debian

77. Compiling Wine 1.4-rc4 and wine 1.4-rc5 on debian testing

24 February 2012

76. Tomato router and free dns

75. [solved] Problems with homebuilt nwchem 6.1 on Debian Testing

74. Building nwchem 6.1 on debian testing 32 bit only

23 February 2012

73. Gnu screen- attach to a running screen session

72. Building maxima from source on Debian Testing

71. Building Thunderbird 10.0.2 on debian testing

20 February 2012

70. Installing Debian on a USB stick -- live usb vs a true and full installation

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