Re: Spring

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Carsten Sachse

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Jul 9, 2014, 8:44:27 AM7/9/14

to misha.ku...@gmail.com, emsp...@googlegroups.com

Dear Misha,

Yes, CTFTILT crashes on this particular micrograph here. I don't have much control over this because it is CTFTILT but you could de-select the CTFTILT refinement step because CTFFIND worked for that micrograph. CTFFIND should be close enough. Or you just throw out this micrograph entirely.

Best wishes,

Carsten

PS For this kind of questions please use https://groups.google.com/forum/#!forum/emspring

On Jul 9, 2014, at 12:49, Misha Kudryashev wrote:

Hi Carsten ,

It was a great meeting down there in Spain, after I am back I got more excited to do some more helical reconstruction with Spring, got some data and when I do CTF correction i get a crash every time. the report follows. It used to work before for my other datasets. Have you ever seen it before?

my pixel size is 0.61 A.

After some micrographs are preocessed it throws an error to the terminal and freezes. (below)

Any ideas how I could fix it?

or maybe is there a way that I could incorparate the outputs from single files into a spring.db?

best,
Misha

bash-4.1$ *** glibc detected *** ctftilt_mp.exe: double free or corruption (out): 0x0000000000efea00 ***

======= Backtrace: =========
/lib64/libc.so.6[0x3490c76166]

/lib64/libc.so.6[0x3490c78c93]
ctftilt_mp.exe[0x411c7a]

ctftilt_mp.exe[0x4133d8]
ctftilt_mp.exe[0x41a2c1]

/lib64/libc.so.6(__libc_start_main+0xfd)[0x3490c1ed1d]
ctftilt_mp.exe[0x402429]

======= Memory map: ========
00400000-00456000 r-xp 00000000 00:27f 3196948 /net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/parts/ctf/bin/ctftilt_mp.exe

00655000-0068a000 rw-p 00055000 00:27f 3196948 /net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/parts/ctf/bin/ctftilt_mp.exe

0068a000-006bc000 rw-p 00000000 00:00 0
00ef7000-00f25000 rw-p 00000000 00:00 0 [heap]

3490400000-3490420000 r-xp 00000000 08:05 1835424 /lib64/ld-2.12.so
349061f000-3490620000 r--p 0001f000 08:05 1835424 /lib64/ld-2.12.so

3490620000-3490621000 rw-p 00020000 08:05 1835424 /lib64/ld-2.12.so
3490621000-3490622000 rw-p 00000000 00:00 0

3490c00000-3490d8b000 r-xp 00000000 08:05 1835425 /lib64/libc-2.12.so
3490d8b000-3490f8a000 ---p 0018b000 08:05 1835425 /lib64/libc-2.12.so

3490f8a000-3490f8e000 r--p 0018a000 08:05 1835425 /lib64/libc-2.12.so
3490f8e000-3490f8f000 rw-p 0018e000 08:05 1835425 /lib64/libc-2.12.so

3490f8f000-3490f94000 rw-p 00000000 00:00 0
3491000000-3491017000 r-xp 00000000 08:05 1835426 /lib64/libpthread-2.12.so

3491017000-3491217000 ---p 00017000 08:05 1835426 /lib64/libpthread-2.12.so
3491217000-3491218000 r--p 00017000 08:05 1835426 /lib64/libpthread-2.12.so

3491218000-3491219000 rw-p 00018000 08:05 1835426 /lib64/libpthread-2.12.so
3491219000-349121d000 rw-p 00000000 00:00 0

3491400000-3491407000 r-xp 00000000 08:05 1835427 /lib64/librt-2.12.so
3491407000-3491606000 ---p 00007000 08:05 1835427 /lib64/librt-2.12.so

3491606000-3491607000 r--p 00006000 08:05 1835427 /lib64/librt-2.12.so
3491607000-3491608000 rw-p 00007000 08:05 1835427 /lib64/librt-2.12.so

3491800000-3491883000 r-xp 00000000 08:05 1835449 /lib64/libm-2.12.so
3491883000-3491a82000 ---p 00083000 08:05 1835449 /lib64/libm-2.12.so

3491a82000-3491a83000 r--p 00082000 08:05 1835449 /lib64/libm-2.12.so
3491a83000-3491a84000 rw-p 00083000 08:05 1835449 /lib64/libm-2.12.so

7f3e24000000-7f3e24282000 rw-p 00000000 00:00 0
7f3e24282000-7f3e28000000 ---p 00000000 00:00 0

7f3e2c000000-7f3e2c282000 rw-p 00000000 00:00 0
7f3e2c282000-7f3e30000000 ---p 00000000 00:00 0

7f3e34000000-7f3e34182000 rw-p 00000000 00:00 0
7f3e34182000-7f3e38000000 ---p 00000000 00:00 0

7f3e3c000000-7f3e3c282000 rw-p 00000000 00:00 0
7f3e3c282000-7f3e40000000 ---p 00000000 00:00 0

7f3e44000000-7f3e44182000 rw-p 00000000 00:00 0
and so on...

the report looks like

working working working and then:

INFO:CPU3:assemble_diagnostic_plot:Diagnostics for 47kx_60epa2_30i_173_aligned.mrc:
CTFFIND montage added to diagnostic output plot.
CTFTILT montage added to diagnostic output plot.
Essential CTFFIND report output added to diagnostic output plot.
Essential CTFTILT report output added to diagnostic output plot.

INFO:CPU3:assemble_diagnostic_plot:progress state: 27 % [==========> ]
INFO:CPU2:run_ctffind_for_first_defocus_estimation:progress state: 25 % [==========> ]

INFO:CPU2:run_ctftilt_to_refine_defocus_parameters:

File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/bin/micctfdetermine_mpi", line 125, in <module>
sys.exit(spring.micprgs.micctfdetermine_mpi.main())

File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/lib/python2.7/site-packages/emspring-0.82.1339dev-py2.7.egg/spring/micprgs/micctfdetermine_mpi.py", line 179, in main
micrograph.determine_ctf()

File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/lib/python2.7/site-packages/emspring-0.82.1339dev-py2.7.egg/spring/micprgs/micctfdetermine_mpi.py", line 167, in determine_ctf
self.run_ctffind_and_ctftilt_for_given_micrographs(self.micrograph_files, self.outfiles)

File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/lib/python2.7/site-packages/emspring-0.82.1339dev-py2.7.egg/spring/micprgs/micctfdetermine_mpi.py", line 121, in run_ctffind_and_ctftilt_for_given_micrographs

each_micrograph_file)
File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/lib/python2.7/site-packages/emspring-0.82.1339dev-py2.7.egg/spring/micprgs/micctfdetermine.py", line 656, in run_ctffind_and_ctftilt_for_each_micrograph

self.run_ctffind_for_first_defocus_estimation(each_micrograph_file)
File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/lib/python2.7/site-packages/emspring-0.82.1339dev-py2.7.egg/spring/micprgs/micctfdetermine.py", line 416, in run_ctffind_for_first_defocus_estimation

ctffind_report_file, find_power_montage = self.launch_ctffind(micrograph_file)
File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/lib/python2.7/site-packages/emspring-0.82.1339dev-py2.7.egg/spring/micprgs/micctfdetermine.py", line 310, in launch_ctffind

self.start_program_and_capture_output(find_power_montage, ctffind_exe, script, ctffind_report_file)
File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/lib/python2.7/site-packages/emspring-0.82.1339dev-py2.7.egg/spring/micprgs/micctfdetermine.py", line 264, in start_program_and_capture_output

log_stdout, log_stderr = ctftilt_process.communicate(input=script)
File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/parts/EMAN2/Python/lib/python2.7/subprocess.py", line 751, in communicate

return self._communicate(input)
File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/parts/EMAN2/Python/lib/python2.7/subprocess.py", line 1291, in _communicate
stdout, stderr = self._communicate_with_poll(input)

File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/parts/EMAN2/Python/lib/python2.7/subprocess.py", line 1345, in _communicate_with_poll
ready = poller.poll()

--
Misha Kudryashev, PhD
Biozentrum, University of Basel
Mattenstrasse 26
CH-4058 Basel, Switzerland
tel: +41 61 387 32 32
email:mikhail.k...@unibas.ch
web: www.c-cina.unibas.ch

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