[Mrtrix-discussion] mrtrix in CentOS

Tue Jul 30 11:10:15 PDT 2013

Hello mrtrixers.

The issue of running mrtrix on a non-debian OS has come up before in this
list. As we have access to a moderately large cluster that we want to use
but that unfortunately does not run a debian flavor, we had to do something
about it.

The always up to date instructions are
here<https://docs.google.com/document/d/1b1d--oSQXb29FVPZFpwD1Wuj0nIDUK1allN4ceXoOSc/edit?usp=sharing>
:
https://docs.google.com/document/d/1b1d--oSQXb29FVPZFpwD1Wuj0nIDUK1allN4ceXoOSc/edit?usp=sharing

and are copied below as a reference to the list users. While it is not
immediately user-friendly, it is not as hard once all dependencies are met.
It is working like a charm for us, and it sure beats having to replace the
OS on the computing cluster!

Full credit and kudos go to Edgar Morales, who configured and documented
all of this work. I hope this ensures that no mrtrixer is left behind due
to an OS incompatibility.

Cheers!

Dr. Luis Concha
Instituto de Neurobiología
Laboratorio C-13
UNAM, Campus Juriquilla
Boulervard Juriquilla 3001
Juriquilla, Querétaro.
C.P. 76230
México
Tel (442) 2 38 10 54
Fax (442) 2 38 10 46
www.inb.unam.mx

-------------------------------------------------------------
Begin instructions
--------------------------------------------------------------

The problem of dependences for mrtrix in CentOS 5.2 can be solved using
schroot with a debian distribution that has the possibility to use the
neurodebian repositories. The approximation that resulted best for us, was
to compile all the programs that are needed in a virtual machine with
CentOS 5.2, specifically we use virtualbox to virtualize the operative
system.

First we compile schroot, so we need to download the
schroot-1.1.5-4.src.rpm  source package from
http://www.nikhef.nl/~dennisvd/schroot.html.

In CentOS is necessary to install this libraries:
yum install rpmbuild  boost boost-devel pam-devel e2fsprogs-devel
lock-devel gcc-c++ make lockdev-devel gcc kernel-devel yum groupinstall
“Development Tools”

Then we need to install the schroot package
rpm -i schroot-1.1.5-4.src.rpm

At this point there was a problem  with the installation, which we solved
it with the creation of the redhat directory in /usr/src/ but google found
yet another solution which was not tested by us. The solution mentioned the
use of the option nomd5
rpm --nomd5 -i schroot-1.1.5-4.src.rpm

After the source is install is necessary change directory to SPECS  inside
the redhat directory and compile schroot:

cd /usr/src/redhat/SPECS

rpmbuild -bb schroot.spec

Then in the  build directory we can find the schroot rpm package and the
last step is to install it

rpm -Uvh schroot-1.1.5-4.x86_64.rpm

The program debootstrap was downloaded from
http://pkgs.org/centos-5-rhel-5/epel-i386/debootstrap-1.0.7-3.el5.noarch.rpm.html

and the installation was straightforward
rpm -Uvh debootstrap-1.0.7-3.el5.noarch.rpm

After this step we create a directory for the chroot and use debootstrap to
download the chroot. Is important to notice that the lenny distribution
worked perfectly by using the archive repositories of debian. However, in
order to install squeeze and have a newer version of mrtrix, it is
necessary to create a symbolic link for squeeze in the
/usr/lib/debootstrap/scripts

ln -s /usr/lib/debootstrap/scripts/sid /usr/lib/debootstrap/scripts/squeeze

Using debootstrap to install chroot we download the entire operating
system. This command installs the OS in the directory that we recently
create.

 For Lenny:

debotstrap --arch amd64 lenny lenny/ http://archive.debian.org/debian

For Squeeze:

 debotstrap --arch amd64 squeeze squeeze/ http://ftp.us.debian.org/debian

Now we can modify the /etc/schroot/schroot.conf in order to include the
chroot recently installed.

[lenny]
description=Debian Lenny
type=directory
location=/home/user/lenny
priority=3
users=YOUR_USER
groups=SOME_GROUP_LIKE_users
root-groups=YOUR_ADMIN_USER
run-setup-scripts=true
run-exec-scripts=true

In order to have internet acces is necesary to copy /etc/resolv.conf to the
etc of the chroot something like:

cp  /etc/resolv.conf /home/user/lenny/etc/

To get inside chroot we need to use the command :

schroot -c lenny

and it will give us a debian terminal where we can update and upgrade the
system.

To install mrtrix we need to use the neurodebian repository
>wget -O- http://neuro.debian.net/lists/squeeze.de-m.full | sudo tee
/etc/apt/sources.list.d/neurodebian.sources.list
>sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9

If we use Lenny is necessary to change the neurodebian.sources.list and
change squeeze for lenny.

deb http:\\neurodebian.ovgu.de/debian lenny main contrib non free

Now we can install mrtrix by typing:

>sudo apt-get update >sudo apt-get upgrade >sudo apt-get install mrtrix

We can add the path for the binaries and libraries
>export
PATH=/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin:/usr/lib/mrtrix/bin
>
export LD_LIBRARY_PATH=/usr/lib/mrtrix/lib

At this point is easy to run the mrtrix binaries inside chroot, but it is
possible to run them outside the chroot:

schroot -p -c lenny/  /usr/lib/mrtrix/bin/streamtrack   I: [lenny chroot]
Running command:“/usr/lib/mrtrix/bin/streamtrack”   streamtrack:expected
exactly 3 arguments (0 supplied)

So, here we are, issuing an mrtrix command from CentOS, but the actual
command gets run by debian, transparently to the user. We have tested this
even on a SunGridEngine cluster, and it works like a charm.

Note that if  you are using a computing cluster, then schroot must be
installed in every executing node, and schroot.conf must point to the
chroot, which must be accessible to the node.

For each executing node:

Install boost libraries:

yum install boost

Update

bzip2-libs x86_64

Also install the following dependencies:

libicu

bzip2-libs i386

And accept the GPG key:

http://mirror.centos.org/centos/RPM-GPG-KEY-CentOS-5

<http://mirror.centos.org/centos/RPM-GPG-KEY-CentOS-5>

Install lockdev

yum install lockdev

Install schroot

rpm -Uvh schroot-1.1.5-4.x86_64.rpm

and, finally, edit etc/schroot/schroot.conf to point to the chroot, as
described above. This node is ready to run debian!
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