Bug #1524: applyctf from EMAN 1.9 release causes strip in the corrected image when installed on CentOS 6 - Appion - Electron Microscopy Group

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Bug #1524

closed

applyctf from EMAN 1.9 release causes strip in the corrected image when installed on CentOS 6

Added by Anchi Cheng almost 13 years ago. Updated over 11 years ago.

Status:

Closed

Priority:

Normal

Assignee:

Sargis Dallakyan

Category:

Installation

Target version:

Appion/Leginon 3.0.0

Start date:

01/17/2012

Due date:

% Done:

Estimated time:

Affected Version:

Appion/Leginon 2.2.0

Show in known bugs:

Workaround:

Description

unknown error. It looks like this

from a command like this:

applyctf /ami/data00/leginon/12jan12z/rawdata/12jan12z_06jul12a_00015gr_00028sq_00004hl_00002en.mrc out-ctfcorrect.mrc parm=-2.594319,200,1,0.159,0,17.4,9,1.53,120,2.0,1.000000 setparm flipphase

I reported it to EMAN team and was advised to try the daily build. The 2012-Jan-15 build worked.

Regarding bug fix of the release, here is the reply from Grant Tang <gtang@bcm.edu>

You can use EMAN daily release safely because we do not do much
development for EMAN1 unless important bu fix.

Grant

>On Tue, 2012-01-17 at 12:56 -0600, Anchi Cheng wrote:
>Please let me know when this bug fix makes
>it into the release so that we can re-direct people to install
>that instead.

To do: replace Appion redmine attachment to the daily build.

Files

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out-ctfcorrect.jpg (341 KB) out-ctfcorrect.jpg		Anchi Cheng, 01/17/2012 11:30 AM
start.hed (2 KB) start.hed		Anchi Cheng, 03/07/2012 11:27 AM
start.img (200 KB) start.img		Anchi Cheng, 03/07/2012 11:27 AM
lp.hed (2 KB) lp.hed		Anchi Cheng, 03/07/2012 11:27 AM
lp.img (200 KB) lp.img		Anchi Cheng, 03/07/2012 11:27 AM

Related issues 4 (1 open — 3 closed)

Related to Appion - Task #1513: CentOS 6 installation of myami 3.0 errors

Closed

Anchi Cheng

01/18/2012

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Related to Appion - Task #1517: new installation instruction for myami 2.2

Closed

Amber Herold

01/12/2012

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Related to Appion - Feature #1757: use eman2 in makestack2.py

Assigned

Anchi Cheng

04/23/2012

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Blocked by Appion - Bug #1827: EMAN1 produces artifacts on CentOS 6

Closed

Amber Herold

05/29/2012

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Issue # Delay: days Cancel

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Updated by Anchi Cheng almost 13 years ago

more e-mail from Steve Ludtke

Hi Anchi. EMAN1 hasn't been actively developed for ~5 years, and has been formally deprecated for ~1 year now. We continue 
to update the nightly snapshots, and occasionally fix small bugs (or tweak File I/O), but don't plan on any more formal 
EMAN1 releases.

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Updated by Anchi Cheng almost 13 years ago

Sargis,

Please try compiling EMAN1 daily build on CentOS 6 to see if the problem can be solved. EMAN1 needs fftw2 while we use fftw3 in Appion python code, so be aware of possible comflict.

However, Steve Lukte said it would not be a problem as they would carry different names.

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Updated by Sargis Dallakyan almost 13 years ago

Assignee changed from Amber Herold to Sargis Dallakyan

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Updated by Anchi Cheng over 12 years ago

We have artifact problem on proc2d for simple manipulation like shrink as well. This is bad.

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Updated by Sargis Dallakyan over 12 years ago

Status changed from Assigned to Won't Fix or Won't Do

Thank you Anchi. I installed EMAN1 (1.9) from source (including fftw2) on 64-bit CentOS 6. This problems is still there. 32-bit binaries work fine on 64-bit CentOS 6. Will use pre-compiled 32-bit binaries for EMAN1 for now.

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Updated by Anchi Cheng over 12 years ago

E-mail from EMAN team member Grant Tang (We have CentOS 6.2):

Hi, Anchi:

Your test case is very precious to track this problem down. This artifact problem does not show up on the computer I used to produce EMAN 64 bit binary. I also tested to install this binary on more than a dozen of different Linux system. It looks like most possibly this is due to a bug in the some version of gcc library, libstdc++ to be specifically.

Two versions of Linux system can reproduce this issue:

Fedora 14 x86_64, gcc version 4.5.1-4.fc14
CentOS 6.2 x86_64, gcc version 4.4.6-3.el6

And this problem is limited to redhat/fedora/centos system only. For example, The OpenSuSE 11.04 has gcc 4.5.1 but does not have this problem.

When you say the problem is on CentOS6. I guess you already updated your system to CentOS6.2 since this issue does not show up on CentOS6 (I did not test it on 6.1).

My suggestion would be to avoid using EMAN1 on 64bit Fedora14 and CentOS6.2 system.

Grant

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Updated by Anchi Cheng over 12 years ago

File start.hed start.hed added
File start.img start.img added
File lp.hed lp.hed added
File lp.img lp.img added

Here is the test case I sent him:

It turns out that we get artifact in low pass filtering with proc2d as well, so the test case used this command:

proc2d start.hed lp.hed apix=1.64 lp=10

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Updated by Neil Voss over 12 years ago

I tried Anchi's test on 3 of my computers running both CentOS 6.2 and Fedora 16 on both Intel and Athlon machines, no artifacts.

Link to image:
https://emportal.scripps.edu/myami/imgreport.php?id=1770361&preset=all

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Updated by Neil Voss over 12 years ago

no artifacts in the CTF correction either.

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#10

Updated by Neil Voss over 12 years ago

Fedora 16:

ldd /data01/prog/eman1/bin/proc2d
    linux-vdso.so.1 =>  (0x00007fff7dbff000)
    libEM.so => /usr/local/EMAN/lib/libEM.so (0x00007f3674443000)
    libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003e1ba00000)
    libm.so.6 => /lib64/libm.so.6 (0x0000003e16a00000)
    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003e17600000)
    libc.so.6 => /lib64/libc.so.6 (0x0000003e15e00000)
    /lib64/ld-linux-x86-64.so.2 (0x0000003e15a00000)

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#11

Updated by Anchi Cheng over 12 years ago

Status changed from Won't Fix or Won't Do to Assigned
Target version changed from Appion/Leginon 2.2.0 to Appion/Leginon 3.0.0

Sargis,

Could you give it a try again. If it still does not work on your test machine, please find out from Neil what is needed so that we will have a working version when guppy moves to CentOS 6.2. We still have too many functions that depends on EMAN1

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#12

Updated by Anchi Cheng over 12 years ago

see update from Neil on Issue #1757 for more details

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#13

Updated by Sargis Dallakyan over 12 years ago

Thank you Anchi and Neil. I run the latest nightly EMAN 1.9 ($Date: 2012/04/23 17:01:03 $) and the artifact problem no longer shows up. I'm currently using the same version of CentOS as Neil is using (CentOS 6.2 x86_64, gcc version 4.4.6-3.el6).


$ ldd /opt/EMAN/bin/proc2d
    linux-vdso.so.1 =>  (0x00007fffc0fff000)
    libEM.so => /opt/EMAN/lib/libEM.so (0x00007f7b9928b000)
    libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003d17600000)
    libm.so.6 => /lib64/libm.so.6 (0x0000003d10e00000)
    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003d17200000)
    libc.so.6 => /lib64/libc.so.6 (0x0000003d11200000)
    /lib64/ld-linux-x86-64.so.2 (0x0000003d10a00000)

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#14

Updated by Anonymous over 12 years ago

So the good news: the x86_64 cluster binaries of proc2d worked for me on Ubuntu 12.04 on some old '08 Xeons and newer '12 Xeons. At least they do with Anchi's test case.

The bad news is: I only found this out after saying "screw it" while trying to get EMAN compiled from source on Ubuntu 12.04. I was having problems linking to newer versions of Python and Qt, etc. With enough work someone could get it to work probably, but...

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#15

Updated by Neil Voss over 12 years ago

Craig, I highly recommend using the "nightly build" source code checkout. It fixes a lot of the newer software conflicts.

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#16

Updated by Anchi Cheng over 12 years ago

Status changed from Assigned to Merge

Sargis helped me to do yum update on the 3.0 developing laptop. After that, the nightly-built works there, too. Looks like we can close this issue now.

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#17

Updated by Amber Herold over 11 years ago

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

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Bug #1524

applyctf from EMAN 1.9 release causes strip in the corrected image when installed on CentOS 6

Updated by Anchi Cheng almost 13 years ago

Updated by Anchi Cheng almost 13 years ago

Updated by Sargis Dallakyan almost 13 years ago

Updated by Anchi Cheng over 12 years ago

Updated by Sargis Dallakyan over 12 years ago

Updated by Anchi Cheng over 12 years ago

Updated by Anchi Cheng over 12 years ago

Updated by Neil Voss over 12 years ago

Updated by Neil Voss over 12 years ago

Updated by Neil Voss over 12 years ago

Updated by Anchi Cheng over 12 years ago

Updated by Anchi Cheng over 12 years ago

Updated by Sargis Dallakyan over 12 years ago

Updated by Anonymous over 12 years ago

Updated by Neil Voss over 12 years ago

Updated by Anchi Cheng over 12 years ago

Updated by Amber Herold over 11 years ago