Appion

Hi there!

We have a fresh install of centOS6 and the first thing we ran was the auto install script logged as root as:

python centosAutoInstallation.py

At the bottom of this message is the output of the command above which breaks with a python error:
IOError: [Errno 2] No such file or directory: '/tmp/myami/leginon/leginon.cfg.template'

It seems that it needs leginon first. Is that correct?!

Please, let us know how to proceed from here.
Thanks!

M.

---- output of python centosAutoInstallation.py -----

[root@charon0 Downloads]# python centosAutoInstallation.py
Current OS Information: CentOS release 6.6 (Final)
"root" access checked success... ====================================
Installing job submission server
Installing processing server
Installing database server
Installing web server ====================================

Please enter the registration key. You must be registered at http://ami.scripps.edu/redmine to recieve a registration key: smile!
Registration Key confirmed.
Please enter an email address: mtswulius@gmail.com
Please enter the system root password: ****
Please enter your timezone based on the available options listed at http://www.php.net/manual/en/timezones.php :
Would you like to install EMAN, Xmipp, and Spider at this time?(Y/N): Y
Updating system files....
rpm -Uvh http://dl.fedoraproject.org/pub/epel/6/`uname -i`/epel-release-6-8.noarch.rpm

Please wait......(This may take a few minutes.)

Retrieving http://dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm
Preparing... ##################################################

package epel-release-6-8.noarch is already installed
yum -y update yum*

Please wait......(This may take a few minutes.)

Loaded plugins: fastestmirror, refresh-packagekit, security
Setting up Update Process
Loading mirror speeds from cached hostfile * base: centos-mirror.jchost.net * epel: mirror.hmc.edu * extras: mirrors.easynews.com * updates: linux.mirrors.es.net
No Packages marked for Update

yum -y install yum-fastestmirror.noarch yum-utils.noarch

Please wait......(This may take a few minutes.)

Loaded plugins: fastestmirror, refresh-packagekit, security
Setting up Install Process
Loading mirror speeds from cached hostfile * base: centos.host-engine.com * epel: mirror.hmc.edu * extras: mirrors.easynews.com * updates: linux.mirrors.es.net
No package yum-fastestmirror.noarch available.
Package yum-utils-1.1.30-30.el6.noarch already installed and latest version
Nothing to do

yum -y update

Please wait......(This may take a few minutes.)

Loaded plugins: fastestmirror, refresh-packagekit, security
Setting up Update Process
Loading mirror speeds from cached hostfile * base: centos.host-engine.com * epel: mirror.hmc.edu * extras: mirrors.easynews.com * updates: linux.mirrors.es.net
No Packages marked for Update

yum -y install subversion

Please wait......(This may take a few minutes.)

Loaded plugins: fastestmirror, refresh-packagekit, security
Setting up Install Process
Loading mirror speeds from cached hostfile * base: centos.host-engine.com * epel: mirror.hmc.edu * extras: mirrors.easynews.com * updates: linux.mirrors.es.net
Package subversion-1.6.11-12.el6_6.x86_64 already installed and latest version
Nothing to do

svn co http://ami.scripps.edu/svn/myami/branches/myami-3.1 /tmp/myami/

Please wait......(This may take a few minutes.)

svn: OPTIONS of 'http://ami.scripps.edu/svn/myami/branches/myami-3.1': Could not resolve hostname `ami.scripps.edu': Host not found (http://ami.scripps.edu)
yum -y install torque-server torque-scheduler

Please wait......(This may take a few minutes.)

Loaded plugins: fastestmirror, refresh-packagekit, security
Setting up Install Process
Loading mirror speeds from cached hostfile * base: centos.host-engine.com * epel: mirror.hmc.edu * extras: mirrors.easynews.com * updates: linux.mirrors.es.net
Package torque-server-4.2.10-3.el6.x86_64 already installed and latest version
Package torque-scheduler-4.2.10-3.el6.x86_64 already installed and latest version
Nothing to do

Warning: /var/lib/torque/server_priv/nodes not found.

yum -y install ImageMagick MySQL-python compat-gcc-34-g77 fftw3-devel gcc-c++ gcc-gfortran gcc-objc gnuplot grace gsl-devel libtiff-devel netpbm-progs numpy openmpi-devel python-devel python-imaging python-matplotlib python-tools scipy wxPython xorg-x11-server-Xvfb libjpeg-devel zlib-devel

Please wait......(This may take a few minutes.)

Loaded plugins: fastestmirror, refresh-packagekit, security
Setting up Install Process
Loading mirror speeds from cached hostfile * base: centos.host-engine.com * epel: mirror.hmc.edu * extras: mirrors.easynews.com * updates: linux.mirrors.es.net
Package ImageMagick-6.5.4.7-7.el6_5.x86_64 already installed and latest version
Package MySQL-python-1.2.3-0.3.c1.1.el6.x86_64 already installed and latest version
Package compat-gcc-34-g77-3.4.6-19.el6.x86_64 already installed and latest version
Package fftw-devel-3.2.1-3.1.el6.x86_64 already installed and latest version
Package gcc-c++-4.4.7-11.el6.x86_64 already installed and latest version
Package gcc-gfortran-4.4.7-11.el6.x86_64 already installed and latest version
Package gcc-objc-4.4.7-11.el6.x86_64 already installed and latest version
Package gnuplot-4.2.6-2.el6.x86_64 already installed and latest version
Package grace-5.1.22-7.el6.x86_64 already installed and latest version
Package gsl-devel-1.13-1.el6.x86_64 already installed and latest version
Package libtiff-devel-3.9.4-10.el6_5.x86_64 already installed and latest version
Package netpbm-progs-10.47.05-11.el6.x86_64 already installed and latest version
Package numpy-1.4.1-9.el6.x86_64 already installed and latest version
Package openmpi-devel-1.8.1-1.el6.x86_64 already installed and latest version
Package python-devel-2.6.6-52.el6.x86_64 already installed and latest version
Package python-imaging-1.1.6-19.el6.x86_64 already installed and latest version
Package python-matplotlib-0.99.1.2-1.el6.x86_64 already installed and latest version
Package python-tools-2.6.6-52.el6.x86_64 already installed and latest version
Package scipy-0.7.2-8.el6.x86_64 already installed and latest version
Package wxPython-2.8.12.0-1.el6.x86_64 already installed and latest version
Package xorg-x11-server-Xvfb-1.15.0-26.el6.centos.0.1.x86_64 already installed and latest version
Package libjpeg-turbo-devel-1.2.1-3.el6_5.x86_64 already installed and latest version
Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest version
Nothing to do

which mpirun

Please wait......(This may take a few minutes.)

which: no mpirun in (/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/local/bin:/usr/bin:/bin:/usr/bin/appion:/root/bin:/usr/bin/appion)
locate mpirun

Please wait......(This may take a few minutes.)

wget -c http://launchpad.net/pyfftw/trunk/0.2.2/+download/PyFFTW3-0.2.2.tar.gz

Please wait......(This may take a few minutes.)

--2015-07-15 17:33:36-- http://launchpad.net/pyfftw/trunk/0.2.2/+download/PyFFTW3-0.2.2.tar.gz
Resolving launchpad.net... 91.189.89.223, 91.189.89.222
Connecting to launchpad.net|91.189.89.223|:80... connected.
HTTP request sent, awaiting response... 303 See Other
Location: https://launchpadlibrarian.net/86827749/PyFFTW3-0.2.2.tar.gz [following]
--2015-07-15 17:33:37-- https://launchpadlibrarian.net/86827749/PyFFTW3-0.2.2.tar.gz
Resolving launchpadlibrarian.net... 91.189.89.229, 91.189.89.228
Connecting to launchpadlibrarian.net|91.189.89.229|:443... connected.
HTTP request sent, awaiting response... 200 OK

The file is already fully retrieved; nothing to do.

tar -zxvf PyFFTW3-0.2.2.tar.gz

Please wait......(This may take a few minutes.)

PyFFTW3-0.2.2/
PyFFTW3-0.2.2/COPYING
PyFFTW3-0.2.2/README.txt
PyFFTW3-0.2.2/PKG-INFO
PyFFTW3-0.2.2/test/
PyFFTW3-0.2.2/test/test_fftw3.py
PyFFTW3-0.2.2/test/test_fftw3_threads.py
PyFFTW3-0.2.2/setup.py
PyFFTW3-0.2.2/src/
PyFFTW3-0.2.2/src/templates/
PyFFTW3-0.2.2/src/templates/planning.tmpl.py
PyFFTW3-0.2.2/src/templates/wisdom.tmpl.py
PyFFTW3-0.2.2/src/templates/__init__.py
PyFFTW3-0.2.2/src/templates/lib.tmpl.py
PyFFTW3-0.2.2/AUTHORS

python setup.py install

Please wait......(This may take a few minutes.)

fftw3 is not located at /usr/lib/libfftw3.so, trying util.find_library(fftw3)
found fftw3 at libfftw3.so.3
fftw3f is not located at /usr/lib/libfftw3f.so, trying util.find_library(fftw3f)
found fftw3f at libfftw3f.so.3
fftw3l is not located at /usr/lib/libfftw3l.so, trying util.find_library(fftw3l)
found fftw3l at libfftw3l.so.3
running install
running build
running build_py
build build/lib/fftw3/lib.py from template src/templates/lib.tmpl.py
build build/lib/fftw3/wisdom.py from template src/templates/wisdom.tmpl.py
build build/lib/fftw3/planning.py from template src/templates/planning.tmpl.py
build build/lib/fftw3f/lib.py from template src/templates/lib.tmpl.py
build build/lib/fftw3f/wisdom.py from template src/templates/wisdom.tmpl.py
build build/lib/fftw3f/planning.py from template src/templates/planning.tmpl.py
build build/lib/fftw3l/lib.py from template src/templates/lib.tmpl.py
build build/lib/fftw3l/wisdom.py from template src/templates/wisdom.tmpl.py
build build/lib/fftw3l/planning.py from template src/templates/planning.tmpl.py
running install_lib
copying build/lib/fftw3l/planning.py -> /usr/lib/python2.6/site-packages/fftw3l
copying build/lib/fftw3l/wisdom.py -> /usr/lib/python2.6/site-packages/fftw3l
copying build/lib/fftw3l/lib.py -> /usr/lib/python2.6/site-packages/fftw3l
copying build/lib/fftw3f/planning.py -> /usr/lib/python2.6/site-packages/fftw3f
copying build/lib/fftw3f/wisdom.py -> /usr/lib/python2.6/site-packages/fftw3f
copying build/lib/fftw3f/lib.py -> /usr/lib/python2.6/site-packages/fftw3f
copying build/lib/fftw3/planning.py -> /usr/lib/python2.6/site-packages/fftw3
copying build/lib/fftw3/wisdom.py -> /usr/lib/python2.6/site-packages/fftw3
copying build/lib/fftw3/lib.py -> /usr/lib/python2.6/site-packages/fftw3
byte-compiling /usr/lib/python2.6/site-packages/fftw3l/planning.py to planning.pyc
byte-compiling /usr/lib/python2.6/site-packages/fftw3l/wisdom.py to wisdom.pyc
byte-compiling /usr/lib/python2.6/site-packages/fftw3l/lib.py to lib.pyc
byte-compiling /usr/lib/python2.6/site-packages/fftw3f/planning.py to planning.pyc
byte-compiling /usr/lib/python2.6/site-packages/fftw3f/wisdom.py to wisdom.pyc
byte-compiling /usr/lib/python2.6/site-packages/fftw3f/lib.py to lib.pyc
byte-compiling /usr/lib/python2.6/site-packages/fftw3/planning.py to planning.pyc
byte-compiling /usr/lib/python2.6/site-packages/fftw3/wisdom.py to wisdom.pyc
byte-compiling /usr/lib/python2.6/site-packages/fftw3/lib.py to lib.pyc
running install_egg_info
Removing /usr/lib/python2.6/site-packages/PyFFTW3-0.2.2-py2.6.egg-info
Writing /usr/lib/python2.6/site-packages/PyFFTW3-0.2.2-py2.6.egg-info

./pysetup.sh install

Please wait......(This may take a few minutes.)

/bin/sh: ./pysetup.sh: No such file or directory
python -c "import sys;print sys.prefix"

Please wait......(This may take a few minutes.)

/usr

python setup.py install --install-scripts=/usr/bin/appion

Please wait......(This may take a few minutes.)

python: can't open file 'setup.py': [Errno 2] No such file or directory
Traceback (most recent call last):
File "centosAutoInstallation.py", line 1190, in <module>
a.run()
File "centosAutoInstallation.py", line 1138, in run
result = self.setupProcessServer()
File "centosAutoInstallation.py", line 359, in setupProcessServer
self.setupLeginonCfg()
File "centosAutoInstallation.py", line 714, in setupLeginonCfg
inf = open( configTemplateFile, 'r' )
IOError: [Errno 2] No such file or directory: '/tmp/myami/leginon/leginon.cfg.template'