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LBEM-CH / focus

High Throughput Electron Microscopy Image Processing Software
http://www.focus-em.org
GNU General Public License v2.0
35 stars 14 forks source link

Hangs on process #207

Open ajrzepiela opened 6 years ago

ajrzepiela commented 6 years ago

Focus hangs on any process when a project folder is moved to a different location. However import works OK to the same folder. It is also possible to start the process manually (e.g csh import_serialem.com from project_dir/auto/00000000002/proc; this works) but not from the GUI. In GUI only first line ######import_serialem##### is shown in the log and then process hangs.

Mounting a bigger disk to a project folder where focus was running processes successfully before also causes the same problem. The disk I am trying focus to run on is RAID SSD partition.

What can I try to fix this issue?

sthennin commented 6 years ago

I am not sure if I understand your problem correctly: You ran FOCUS successfully on /diskA/project but then \mv /diskA/project /diskB and then FOCUS didn't correctly run in /diskB ?

The configuration data in FOCUS are retrieved in the following way:

1) FOCUS reads the computer-wide default configs in focus/resources/config/2dx_master.cfg 2) FOCUS overwrites some values with the personal configs in ~/.2dx/2dx.cfg 3) FOCUS overwrites some values with the project-wide configs in /diskA/project/merge/2dx_merge.cfg 4) for values that are not GLOBAL, FOCUS overwrites the values with configs found in the individual image directories.

If you launch a script for one specific image, then FOCUS will know the level-3) values above by reaching out for ../2dx_master.cfg. which normally is a link to the ../merge/2dx_merge.cfg file.

If you move a project to a different disk, then this last symbolic link might be broken.

In this case: Try running the script "Report Project Links", which you find in the top-left PROJECT tab as third button from the left.

ajrzepiela commented 6 years ago

Dear Henning,

Thanks for reply. I do not think I have broken links since I start a project from a scratch.

  1. When I start project in ~/focus/focus_projects/project1 (this is on disk sda) I can import, run processes and Focus is OK.
  2. When I start project in /data/project1 (which is disk sdb, RAID SSD) I can import images but I cannot process them (every process halts at the start).
  3. When I mount the sdb to ~/focus/focus_projects/ I have the same problem as in point 2
  4. I also tried network disks to start a project, but then yet another problem shows up, in particular that I do not have permissions to link to a SCRATCH (which is on /data (sdb) and works OK in point 1) . As far as I see I give full permissions to scratch, normal_scratch and to project directories, but this does not help so far. What else I can try?

Thanks,

Andrzej

sthennin commented 6 years ago

Dear Andrzej, this is strange, but to me sounds like a permission problem on the drive /data/project1.
When you run jobs from the command line, you are presumably running it under bash, and the bash environment variables are set. The scripts are then always starting with

!/bin/csh -fe

so that they may start with different environment variables set. Could there be a difference between starting a csh script from the command line, and starting it from within FOCUS?

Otherwise, write permissions would be the other possible cause I could imagine. FOCUS needs to be able to create output directories in the current image directory, such as LOGS and proc. Do these exist, after launching a job?

Can /bin/csh be found on your system?

ajrzepiela commented 6 years ago

Dear Henning,

We managed to solve the problem by adding HDD disk for the projects directory. With the local HDD all seems to work fine (and we have enough space as we wanted to).

Thanks for the hints.

Best,

Andrzej