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Bug #3312

closed

IOError: [Errno 2] No such file or directory: '/tmp/myami/leginon/leginon.cfg.template'

Added by Matt Swulius over 9 years ago. Updated about 9 years ago.

Status:
Closed
Priority:
Urgent
Assignee:
Carl Negro
Category:
-
Target version:
-
Start date:
07/15/2015
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.1.0
Show in known bugs:
No
Workaround:

Description

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'

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 #1

Updated by Anchi Cheng over 9 years ago

  • Status changed from New to Assigned
  • Assignee set to Anchi Cheng
  • Priority changed from Normal to Immediate
  • Affected Version changed from Appion/Leginon 3.2 to Appion/Leginon 3.1.0

The error comes from our move from TSRI to NYSBC. All references in the autoinstaller and related file to ami.scripps.edu have to be changed to emg.nysbc.org

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 #2

Updated by Anchi Cheng over 9 years ago

This should be fixed now with r18907. Please download the updated centosAutoInstallation.py and try again.

Carl, please confirm my changes.

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 #3

Updated by Anchi Cheng over 9 years ago

  • Status changed from Assigned to In Test
  • Assignee changed from Anchi Cheng to Matt Swulius

Matt,

Assign to you to test. Please update the issue to let us know if it is fixed.

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 #4

Updated by Matt Swulius over 9 years ago

Hi,

I'm sorry, but for some reason all of redmine's emails on this issue were sent to spam and I just figured that out right now. It seems strange since this did not happen when I submitted my other issue just a day prior. I will test things and get back to you as soon as I can.

Matt

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 #5

Updated by Matt Swulius over 9 years ago

I have downloaded the new centosAutoInstallation.py. I first made sure to delete the old one. I even checked the file to make sure the changes you made had been made. All of the ami.scripps.edu's have been changed to emg.nysbc.org.

I am still getting the exact same error. I am logged in as root, FYI. This is correct right?

Thanks,
Matt

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 #6

Updated by Anchi Cheng over 9 years ago

Umm, let's go to the basic.

The key is that it should have performed the command

svn co http://emg.nysbc.org/svn/myami/branches/myami-3.1 /tmp/myami/

Try run that alone. If it gives error, then that is where your problem is.

Yes, autoinstaller needs to be run as root.

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 #7

Updated by Matt Swulius over 9 years ago

Thanks! This appears to have gotten me to the root of the problem. It seems that while running the old version of centosAutoInstallation.py, some directories were written, but didn't contain any of the files the script tried to download (this is my guess). So when I ran the svn command you suggested it spit out an error that there were already folders containing "unversioned" versions of appion and leginon.

Once I deleted those folders in /tmp/myami/ I ran the new installation script and it seems to have worked just fine.

Thanks for your help!

Matt

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 #8

Updated by Anchi Cheng over 9 years ago

  • Status changed from In Test to Assigned
  • Assignee changed from Matt Swulius to Carl Negro
  • Priority changed from Immediate to Urgent

Carl,

Please add commands to remove existing subfolder before getting svn check out in our code so that this does not happen again. Thanks.

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 #9

Updated by Anchi Cheng about 9 years ago

  • Status changed from Assigned to Closed
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