Appion

r19003 adds opencv-python. centosAutoInstallation.py exits with an error:

Could not connect: Access denied for user 'root'@'localhost' (using password: NO)

Adding the list of packages to be included in centosAutoInstallation.py

• Protomo 2.4.1
• i3
• Imagemagick
• FFMPEG
• numpy
• scipy
• PIL
• pylab

Hi Sargis,

Can you update us on the progress of getting Protomo auto-installed by default? Thanks, -Alex

Hi Alex,

I'm committed r19105 that makes it possible for auto-installer to create databases and tables without root password for mysql. The good news that auto-installer now finishes successfully and it opens up working myamiweb and leginon after it's done.

On getting Protomo auto-installed by default, I have 80% of the code written. I hope to finish remaining 20% and commit it before the next Appion hangout.

r19121 implements Protomo installer. I've tested this on one of our servers (fly) and it works as expected.

There are a couple of things related to opencv and mysql, that I can discuss with Anchi before closing this issue.

• opencv.x86_64 in the current CentOS 6 distro is version 2.0.0-12.el6 and it's called cv instead of cv2. Can we change openCVcaller.py#L18 as follows and see if this works?
  

  try:
   import cv2
  except:
   import cv as cv2
  

• mysqld_safe --skip-grant-tables & in the current centosAutoInstallation.py works fine and it allows creating databases and tables without root password, however, it won't survive a reboot. I'm thinking to change auto-installation tool wiki page and ask users to run mysql_secure_installation to set mysql root password and then update their sinedon and myamiweb config files.

If i3cut isn't found, then i3 isn't installed or isn't in the path.

Here's my FFmpeg configuration, which works without issue:

configuration: --enable-gpl --enable-version3 --disable-shared --disable-debug --enable-runtime-cpudetect --enable-libmp3lame --enable-libx264 --enable-libx265 --enable-libwebp --enable-libspeex --enable-libvorbis --enable-libvpx --enable-libfreetype --enable-fontconfig --enable-libxvid --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-gray --enable-libopenjpeg --enable-libopus --enable-libass --enable-gnutls --enable-libvidstab --cc=gcc-4.9

I'm using a 2015 ffmpeg version N-45094-g1932f7e-

The i3cut error is not a problem. i3 has a list of image libraries that it tries to load in a particular order; if the first image library isn't present then it goes to the next one. That's all that error signifies - it found the next one and continued working.

It's been many months since I installed the ffmpeg I use so I don't remember what I did exactly... I'll install it again on my end and report back.

I use the static git version of ffmpeg:

http://johnvansickle.com/ffmpeg/

I just tried the latest 64bit build and it runs perfectly.

Alex,

When protomo2align.py what files should we have and how big relative to the images in raw directory ? Our test run, apart from not getting media files had small files in croase_align and recon. I also only used 12 tilts (1 deg increment centered at 0). would that be a problem ?

The cache directory should be as large as the raw directory.

It shouldn't matter how many tilts you work with as long as it's more than maybe 3 or 5, I'm not sure.

Here is the complete terminal output for a Coarse Alignment run with all options as default (except I set frame_aligned=True): http://pastie.org/private/6hjmylrcctsuo8rezx7tya

Here is the corresponding log file: http://pastie.org/private/cd9ajzxxpw7vvy99szejq

Looks like the output size is reasonable with our small tilt series. Now we are only waiting for a good fftmpeg installation through autoinstaller.

I rewrote the i3 paths in the autoinstaller so that protomo2aligner.py finishes, but throws the 'i3cut: could not load libi3tiffio.so, TiffioModule disabled'. Still working on this

Alex,

Here's the console output from your instructions:

[root@vagrant-centos65 local]# wget http://emg.nysbc.org/attachments/download/4677/series000108_cor.img
--2015-11-14 16:31:41-- http://emg.nysbc.org/attachments/download/4677/series000108_cor.img
Resolving emg.nysbc.org... 172.85.57.157
Connecting to emg.nysbc.org|172.85.57.157|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: “series000108_cor.img.1”

[             <=>                       ] 3,788,920   1.47M/s   in 2.5s

2015-11-14 16:31:44 (1.47 MB/s) - “series000108_cor.img.1” saved [3788920]

[root@vagrant-centos65 local]# i3cut -fmt mrc series000108_cor.img series000108_cor.mrc
i3cut: could not load libi3tiffio.so, TiffioModule disabled
[root@vagrant-centos65 local]# proc3d series000108_cor.mrc series000108_cor.mrc norm
EMAN 1.9 Cluster ($Date: 2009/02/18 05:12:22 $).
Run 'proc3d help' for detailed help.
Original image : 160x160x37 Mean=3.2e-05 Sigma=0.00427 Min=-0.0205 Max=0.0394
Sampling : 1 A/pixel Origin = 0,0,0
Final image : 160x160x37 Mean=4.38e-09 Sigma=1
Sampling : 1 A/pixel Origin = 0,0,0
[root@vagrant-centos65 local]# 3dmod series000108_cor.mrc
-bash: 3dmod: command not found
[root@vagrant-centos65 local]#

Is this the output you were anticipating?

Also, could you post the contents of 'echo $PATH', 'echo $PYTHONPATH', and 'echo $LD_LIBRARY_PATH' on your machine? Thanks

Yes it works fine, you just don't have 3dmod (ie. IMOD) installed.

i3cut -fmt mrc input.img output.mrc just takes the Protomo-specific img file format and converts it to mrc. proc3d then normalizes it so that you can open it up and see it in 3dmod: http://bio3d.colorado.edu/imod/doc/3dmodguide.html#ZapWindow

But you don't have 3dmod installed (which is fine). Open it up in any EM image viewer that you prefer to convince yourself.

bash-4.2$ echo $PATH
/panfs/storage.local/imb/home/ajn10d/bin/screen-4.2.1:/panfs/storage.local/imb/home/ajn10d/bin/automatch_v0.3.1_withdata/bin:/panfs/storage.local/imb/home/ajn10d/bin/Komodo-Edit-8.5.4/bin:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/IMOD/bin:/panfs/storage.local/imb/stagg/software/myami_python/bin:/panfs/storage.local/imb/home/ajn10d/myami3/redux/bin:/panfs/storage.local/imb/home/ajn10d/myami3/appion/bin:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/bin:/panfs/storage.local/imb/home/ajn10d/bin/ffmpeg-git-20150311-64bit-static:/panfs/storage.local/imb/home/sstagg/Komodo-Edit-8/bin:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/Xmipp/bin:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/spider18.15/spider/bin/:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/simple_linux_120521/apps:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/simple_linux_120521/bin:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/relion-1.3/bin:/panfs/storage.local/imb/scratch/software/i3-0.9.6/bin:/panfs/storage.local/imb/scratch/software/i3-0.9.6/bin/linux/x86-64:/panfs/storage.local/imb/scratch/software/protomo-2.4.1/bin:/panfs/storage.local/imb/scratch/software/protomo-2.4.1/bin/linux/x86-64:/panfs/storage.local/imb/home/sstagg/hsource_rss_20100325:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/grigorieff/frealign_v9.11/bin:/panfs/storage.local/imb/home/sstagg/software/rhel61/usr/local/EMAN/bin:/panfs/storage.local/imb/home/sstagg/software/rhel61/usr/local/EMAN2/bin:/opt/hpc/gnu/xalt/bin:/panfs/storage.local/opt/hpc/gnu/openmpi/bin:/opt/hpc/gnu/openmpi/bin:/panfs/storage.local/opt/hpc/gnu/bin:/opt/hpc/gnu/bin:/opt/matlab/2014b/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/panfs/storage.local/imb/home/ajn10d/bin:/panfs/storage.local/imb/home/ajn10d/bin/dynamo:/panfs/storage.local/opt/hpc/gnu/bin:/opt/hpc/gnu/bin:/opt/matlab/2014b/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/panfs/storage.local/imb/home/ajn10d/bin:/opt/hpc/gnu:/panfs/storage.local/opt/hpc/gnu/bin:/opt/hpc/gnu/bin:/opt/matlab/2014b/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/panfs/storage.local/imb/home/ajn10d/bin:/panfs/storage.local/imb/home/ajn10d/bin/dynamo-v-1.1.62_MCR-8.2.0_GLNXA64/matlab/bin:/panfs/storage.local/imb/home/ajn10d/bin/dynamo-v-1.1.62_MCR-8.2.0_GLNXA64/matlab/src:/panfs/storage.local/imb/home/ajn10d/bin/dynamo-v-1.1.62_MCR-8.2.0_GLNXA64/cuda/bin:/panfs/storage.local/imb/home/ajn10d/bin/dynamo-v-1.1.62_MCR-8.2.0_GLNXA64/mpi:/panfs/storage.local/imb/home/ajn10d/bin/dynamo-v-1.1.62_MCR-8.2.0_GLNXA64/examples:/panfs/storage.local/imb/home/ajn10d/bin/dynamo-v-1.1.62_MCR-8.2.0_GLNXA64/doc

bash-4.2$ echo $PYTHONPATH
/panfs/storage.local/imb/home/ajn10d/myami3/appion:/panfs/storage.local/imb/home/ajn10d/myami3/leginon:/panfs/storage.local/imb/home/ajn10d/myami3:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/Xmipp/lib:/panfs/storage.local/imb/scratch/software/protomo-2.4.1/lib/linux/x86-64:/panfs/storage.local/imb/home/sstagg/software/rhel61/usr/local/EMAN/lib:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/bin:/panfs/storage.local/imb/home/sstagg/software/rhel61/usr/local/EMAN2/bin:/panfs/storage.local/imb/home/sstagg/software/rhel61/usr/local/EMAN2/lib:/opt/hpc/gnu/xalt/site:/opt/hpc/gnu/xalt/libexec:/usr/lib64/python2.6/site-packages/openmpi

bash-4.2$ echo $LD_LIBRARY_PATH
/usr/local/cuda-7.0/lib64:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/IMOD/lib:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/IMOD/lib:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/Xmipp/lib:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/relion-1.3/lib:/panfs/storage.local/imb/scratch/software/protomo-2.4.1/lib/linux/x86-64:/panfs/storage.local/imb/scratch/software/lib/linux/x86-64:/panfs/storage.local/imb/stagg/software/rhel61/usr/local/lib:/panfs/storage.local/imb/home/sstagg/software/rhel61/usr/local/EMAN/lib:/panfs/storage.local/imb/home/sstagg/software/rhel61/usr/local/EMAN2/lib:/panfs/storage.local/opt/hpc/gnu/openmpi/lib64:/opt/hpc/gnu/openmpi/lib64:/usr/lib64/openmpi/lib:/panfs/storage.local/opt/hpc/gnu/lib64:/opt/hpc/gnu/lib64:/opt/hpc/gnu/lib64/netcdf-3:/panfs/storage.local/imb/home/ajn10d/bin/MCR_82/v82/runtime/glnxa64:/panfs/storage.local/imb/home/ajn10d/bin/MCR_82/v82/bin/glnxa64:/panfs/storage.local/imb/home/ajn10d/bin/MCR_82/v82/sys/os/glnxa64:/panfs/storage.local/imb/home/ajn10d/bin/MCR_82/v82/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/panfs/storage.local/imb/home/ajn10d/bin/MCR_82/v82/sys/java/jre/glnxa64/jre/lib/amd64/server:/panfs/storage.local/imb/home/ajn10d/bin/MCR_82/v82/sys/java/jre/glnxa64/jre/lib/amd64

r19387 merges protomo related r19374 through r19383 from trunk to 3.2 brunch.