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Bug #1827

closed

EMAN1 produces artifacts on CentOS 6

Added by Neil Voss almost 12 years ago. Updated about 11 years ago.

Status:
Closed
Priority:
Urgent
Assignee:
Amber Herold
Category:
Image Processing
Target version:
-
Start date:
05/29/2012
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.2.0
Show in known bugs:
Yes
Workaround:

Description

Related to bugs #1757 and #1524. I am creating an over-arching issue to keep track of this important issue.

Sometimes downloading a new version fixes the artifacts, but sometimes they return.

I have even compiled EMAN1 from the source code. This affects all programs in EMAN1 including applyctf and most importantly proc2d and proc3d.

Solutions appear to either use EMAN2 e2proc2d OR write our own proc2d like function in appion.


Related issues 2 (1 open1 closed)

Blocks Appion - Feature #1757: use eman2 in makestack2.pyAssignedAnchi Cheng04/23/2012

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Blocks Appion - Bug #1524: applyctf from EMAN 1.9 release causes strip in the corrected image when installed on CentOS 6ClosedSargis Dallakyan01/17/2012

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Actions #1

Updated by Neil Voss almost 12 years ago

After compiling, I noticed that on my AMD machines there was no artifact, but on the Intel machines had an artifact.

I looked at my compile flags and noticed that I had ENABLE_OPTERON set to ON. So, I disabled it and now I do not have any artifacts. I will continue to test.

Actions #2

Updated by Anonymous almost 12 years ago

I'm taking a look at this as well now. Do you have anything else to add since the last update? Does the opteron flag come into play from the eman build system?

Has anyone tried compiling and linking their own fftw2.15? I see that a low pass filter reproducibly creates the artifact in affected systems.

Actions #3

Updated by Neil Voss almost 12 years ago

Hi Craig, the experiment I did was with opteron on, artifacts on my intel, with opteron off, no artifacts any where. We have been running this EMAN1 for 22 days with no problems.

I compiled it with following the standard procedure to compile (per EMAN website) I assume it used my local fftw??? It is like using ccmake as a gui instead of ./configure, but then it is make and make install.

Actions #4

Updated by Anonymous almost 12 years ago

Coolio. What are you running? I'm going to try it out on Ubuntu 12.04.
Did you edit out the Opteron flag from the configure scripts, or from the generated make files?

Actions #5

Updated by Neil Voss almost 12 years ago

I set the flag in the "ccmake" program, its a TUI for setting the flags.

Actions #6

Updated by Anchi Cheng almost 12 years ago

Is everyone happy? I've got mine (Intel64) binary daily-built work on CentOS 6.2 after a yum update. If we all got it installed properly one way or the other, I will close this issue.

Actions #7

Updated by Amber Herold about 11 years ago

  • Status changed from New to Closed
  • Affected Version changed from Appion/Leginon 2.2.0 (trunk) to Appion/Leginon 2.2.0
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