JISCMail - CCPEM Archives

Email discussion lists for the UK Education and Research communities
Subscriber's Corner
Email Lists
CCPEM Archives

CCPEM@JISCMAIL.AC.UK

View:

Message:
[
First
Last
]
By Topic:
[
First
Last
]
By Author:
[
First
Last
]
Font:
Proportional Font
		LISTSERV Archives
		CCPEM Home
		CCPEM September 2019
Options

Subscribe or Unsubscribe
Get Password
Subject:
Re: Buffer Overload on Bayesian Polishing
From:
Takanori Nakane <[log in to unmask]>
Reply-To:
Takanori Nakane <[log in to unmask]>
Date:
Mon, 30 Sep 2019 13:59:42 +0100
Content-Type:
text/plain
Parts/Attachments:
text/plain (246 lines)
Hi,

Are you using the latest version (3.0.7)?

Was "bfactors.star" produced? If so, please send it to me.

Best regards,

Takanori Nakane

> Hi,
>
> I am having a problem running Bayesian Polishing. After loop has been
perfor
> med over all micrographs the job consistently crashes during the “fitting [
> of] B/k-factors” with the error:
>
> *** buffer overflow detected ***:
> /opt/relion3/build/bin/relion_motion_refine terminated
> ======= Backtrace: =========
> /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fc7acff27e5]
> /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7fc7ad09415c]
> /lib/x86_64-linux-gnu/libc.so.6(+0x117160)[0x7fc7ad092160]
> /lib/x86_64-linux-gnu/libc.so.6(+0x1166c9)[0x7fc7ad0916c9]
> /lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0x80)[0x7fc7acff66b0]
> /lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0xc90)[0x7fc7acfc8e00]
> /lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x84)[0x7fc7ad091754]
> /lib/x86_64-linux-gnu/libc.so.6(__sprintf_chk+0x7d)[0x7fc7ad0916ad]
> /opt/relion3/build/bin/relion_motion_refine(_ZN7CPlot2D23ComputeLabelTickSpacingEddPdS0_S0_iNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x50b)[0x46604b]
> /opt/relion3/build/bin/relion_motion_refine(_ZN7CPlot2D20PrecomputeDimensionsEv+0x393)[0x466653]
> /opt/relion3/build/bin/relion_motion_refine(_ZN7CPlot2D20OutputPostScriptPlotENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x4f)[0x46684f]
> /opt/relion3/build/bin/relion_motion_refine(_ZN15FrameRecombiner14weightsFromFCCERKSt6vectorI13MetaDataTableSaIS1_EE+0x19a1)[0x5654c1]
> /opt/relion3/build/bin/relion_motion_refine(_ZN15FrameRecombiner4initERKSt6vectorI13MetaDataTableSaIS1_EEiiidiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEbP16ObservationModelP17MicrographHandler+0x200)[0x566770]
> /opt/relion3/build/bin/relion_motion_refine(_ZN13MotionRefiner3runEv+0x129)[0x47a3c9]
> /opt/relion3/build/bin/relion_motion_refine(main+0x4e)[0x42350e]
> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fc7acf9b830]
> /opt/relion3/build/bin/relion_motion_refine(_start+0x29)[0x424089]
> ======= Memory map: ========
> 00400000-005e2000 r-xp 00000000 08:31 27921408
> /opt/relion3/build/bin/relion_motion_refine
> 007e2000-007e3000 r--p 001e2000 08:31 27921408
> /opt/relion3/build/bin/relion_motion_refine
> 007e3000-007e4000 rw-p 001e3000 08:31 27921408
> /opt/relion3/build/bin/relion_motion_refine
> 007e4000-007e5000 rw-p 00000000 00:00 0
> 024df000-7b1da000 rw-p 00000000 00:00 0
> [heap]
> 7525116c5000-752518368000 rw-p 00000000 00:00 0
> 752525cae000-75252c951000 rw-p 00000000 00:00 0
> 7525335f4000-75253a297000 rw-p 00000000 00:00 0
> 752555523000-752569b0c000 rw-p 00000000 00:00 0
> 752584d98000-7525a6cc7000 rw-p 00000000 00:00 0
> 7525b460d000-7525bb2b0000 rw-p 00000000 00:00 0
> 7525e3e82000-75261a39a000 rw-p 00000000 00:00 0
> 752635626000-75263c2c9000 rw-p 00000000 00:00 0
> 752657555000-75265e1f8000 rw-p 00000000 00:00 0
> 75266bb3e000-752680127000 rw-p 00000000 00:00 0
> 75268da6d000-75269b3b3000 rw-p 00000000 00:00 0
> 7526a8cf9000-7526bd2e2000 rw-p 00000000 00:00 0
> 7526cac28000-7526ecb57000 rw-p 00000000 00:00 0
> 7526ed35d000-7526f4000000 rw-p 00000000 00:00 0
> 7526fa49d000-75272306f000 rw-p 00000000 00:00 0
> 752737658000-75273e2fb000 rw-p 00000000 00:00 0
> 752744f9e000-752766ecd000 rw-p 00000000 00:00 0
> 752774813000-7527b19ce000 rw-p 00000000 00:00 0
> 7527b8671000-7527bf314000 rw-p 00000000 00:00 0
> 7527ccc5a000-75284dc73000 rw-p 00000000 00:00 0
> 75285b5b9000-75286fba2000 rw-p 00000000 00:00 0
> 75287d4e8000-7528c1346000 rw-p 00000000 00:00 0
> 7528cec8c000-7528dc5d2000 rw-p 00000000 00:00 0
> 7528e9f18000-75291978d000 rw-p 00000000 00:00 0
> 75291a6ba000-752928000000 rw-p 00000000 00:00 0
> 75292dd76000-75297f51a000 rw-p 00000000 00:00 0
> 75298135d000-752988000000 rw-p 00000000 00:00 0
> 75298d35d000-752994000000 rw-p 00000000 00:00 0
> 75299a7a6000-7529e52a7000 rw-p 00000000 00:00 0
> 7529e7a17000-7529fc000000 rw-p 00000000 00:00 0
> 752a071d6000-752ae0636000 rw-p 00000000 00:00 0
> 752ae135d000-752ae8000000 rw-p 00000000 00:00 0
> 752aedf7c000-752b38a7d000 rw-p 00000000 00:00 0
> 752b3935d000-752b40000000 rw-p 00000000 00:00 0
> 752b463c3000-752b75c38000 rw-p 00000000 00:00 0
> 752b77a17000-752b8c000000 rw-p 00000000 00:00 0
> 752b90ec4000-752bc73dc000 rw-p 00000000 00:00 0
> 752bc935d000-752bd0000000 rw-p 00000000 00:00 0
> 752bd4d22000-752c18b80000 rw-p 00000000 00:00 0
> 752c1935d000-752c20000000 rw-p 00000000 00:00 0
> 752c264c6000-752c3aaaf000 rw-p 00000000 00:00 0
> 752c3d35d000-752c44000000 rw-p 00000000 00:00 0
> 752c4935d000-752c50000000 rw-p 00000000 00:00 0
> 752c55d3b000-752c8c253000 rw-p 00000000 00:00 0
> 752c8d35d000-752c94000000 rw-p 00000000 00:00 0
> 752c99b99000-752cf1fe0000 rw-p 00000000 00:00 0
> 752cf535d000-752cfc000000 rw-p 00000000 00:00 0
> 752d0135d000-752d08000000 rw-p 00000000 00:00 0
> 752d0d26c000-752d6c356000 rw-p 00000000 00:00 0
> 752d6d35d000-752d74000000 rw-p 00000000 00:00 0
> 752d79c9c000-752e085fb000 rw-p 00000000 00:00 0
> 752e0a0d1000-752e2c000000 rw-p 00000000 00:00 0
> 752e311cd000-752ebfb2c000 rw-p 00000000 00:00 0
> 752ec135d000-752ec8000000 rw-p 00000000 00:00 0
> 752ecd472000-753137263000 rw-p 00000000 00:00 0
> 75313935d000-753140000000 rw-p 00000000 00:00 0
> 753144ba9000-7531524ef000 rw-p 00000000 00:00 0
> 75315342e000-75317c000000 rw-p 00000000 00:00 0
> 753181d64000-7531e0e4e000 rw-p 00000000 00:00 0
> 7531e135d000-7531e8000000 rw-p 00000000 00:00 0
> 7531ee794000-753268b0a000 rw-p 00000000 00:00 0
> 75326935d000-753270000000 rw-p 00000000 00:00 0
> 753276450000-75345f228000 rw-p 00000000 00:00 0
> 75345fa17000-753474000000 rw-p 00000000 00:00 0
> 75347a4b4000-7534b766f000 rw-p 00000000 00:00 0
> 7534b935d000-7534c0000000 rw-p 00000000 00:00 0
> 7534c4fb5000-75363a6ba000 rw-p 00000000 00:00 0
> 7536408ed000-7536bac63000 rw-p 00000000 00:00 0
> 7536bc78b000-7536de6ba000 rw-p 00000000 00:00 0
> 7536e3835000-7537209f0000 rw-p 00000000 00:00 0
> 7537220d1000-7537366ba000 rw-p 00000000 00:00 0
> 75373bc7c000-753881b0c000 rw-p 00000000 00:00 0
> 753883a17000-75388a6ba000 rw-p 00000000 00:00 0
> 75388fa17000-7538a4000000 rw-p 00000000 00:00 0
> 7538aa6de000-7538b8024000 rw-p 00000000 00:00 0
> 7538b935d000-7538c0000000 rw-p 00000000 00:00 0
> 7538c596a000-75397ce9b000 rw-p 00000000 00:00 0
> 75397d35d000-753984000000 rw-p 00000000 00:00 0
> 75398a7e1000-753aae742000 rw-p 00000000 00:00 0
> 753ab135d000-753ab8000000 rw-p 00000000 00:00 0
> 753abc088000-753b8e845000 rw-p 00000000 00:00 0
> 753b9135d000-753b98000000 rw-p 00000000 00:00 0
> 753b9c18b000-753d03f4a000 rw-p 00000000 00:00 0
> 753d04d74000-753d126ba000 rw-p 00000000 00:00 0
> 753d18533000-753d41105000 rw-p 00000000 00:00 0
> 753d420d1000-753d64000000 rw-p 00000000 00:00 0
> 753d69cd7000-753de404d000 rw-p 00000000 00:00 0
> 753de535d000-753dec000000 rw-p 00000000 00:00 0
> 753df1993000-753e6bd09000 rw-p 00000000 00:00 0
> 753e6fa17000-753e766ba000 rw-p 00000000 00:00 0
> 753e7ba17000-753e90000000 rw-p 00000000 00:00 0
> 753e948db000-753f30b80000 rw-p 00000000 00:00 0
> 753f3135d000-753f38000000 rw-p 00000000 00:00 0
> 753f3e4c6000-75402526c000 rw-p 00000000 00:00 0
> 75402535d000-75402c000000 rw-p 00000000 00:00 0
> 754032bb2000-754091c9c000 rw-p 00000000 00:00 0
> 75409535d000-75409c000000 rw-p 00000000 00:00 0
> 7540a135d000-7540a8000000 rw-p 00000000 00:00 0
> 7540acf28000-75419a971000 rw-p 00000000 00:00 0
> 75419d35d000-7541a4000000 rw-p 00000000 00:00 0
> 7541a82b7000-754214ce7000 rw-p 00000000 00:00 0
> 75421535d000-75421c000000 rw-p 00000000 00:00 0
> 75422262d000-75426d12e000 rw-p 00000000 00:00 0
> 75426d35d000-754274000000 rw-p 00000000 00:00 0
> 75427aa74000-75434d231000 rw-p 00000000 00:00 0
> 75434fa17000-754364000000 rw-p 00000000 00:00 0
> 75436935d000-754370000000 rw-p 00000000 00:00 0
> 754375e03000-754433fd7000 rw-p 00000000 00:00 0
> 75443535d000-75443c000000 rw-p 00000000 00:00 0
> 75444191d000-75445cba9000 rw-p 00000000 00:00 0
> 75445d35d000-754464000000 rw-p 00000000 00:00 0
> 75446a4ef000-7545d8f51000 rw-p 00000000 00:00 0
> 7545d935d000-7545e0000000 rw-p 00000000 00:00 0
> 7545e6897000-7546087c6000 rw-p 00000000 00:00 0
> 75460935d000-754610000000 rw-p 00000000 00:00 0
> 75461610c000-754703b55000 rw-p 00000000 00:00 0
> 75470535d000-75470c000000 rw-p 00000000 00:00 0
> 75471149b000-754799157000 rw-p 00000000 00:00 0
> 75479935d000-7547a0000000 rw-p 00000000 00:00 0
> 7547a6a9d000-7547c89cc000 rw-p 00000000 00:00 0
> 7547c935d000-7547d0000000 rw-p 00000000 00:00 0
> 7547d6312000-754850688000 rw-p 00000000 00:00 0
> 75485135d000-754858000000 rw-p 00000000 00:00 0
> 75485dfce000-75486b914000 rw-p 00000000 00:00 0
> 75486ba17000-754880000000 rw-p 00000000 00:00 0
> 754886ba0000-75493742e000 rw-p 00000000 00:00 0
> 75493935d000-754940000000 rw-p 00000000 00:00 0
> 754944d74000-754960000000 rw-p 00000000 00:00 0
> 754965ecb000-754ab29fe000 rw-p 00000000 00:00 0
> 754ab535d000-754abc000000 rw-p 00000000 00:00 0
> 754ac0344000-754af685c000 rw-p 00000000 00:00 0
> 754af742e000-754afe0d1000 rw-p 00000000 00:00 0
> 754affa17000-754b14000000 rw-p 00000000 00:00 0
> 754b1935d000-754b20000000 rw-p 00000000 00:00 0
> 754b260d1000-754b48000000 rw-p 00000000 00:00 0
> 754b48ce7000-754b6ac16000 rw-p 00000000 00:00 0
> 754b6d35d000-754b74000000 rw-p 00000000 00:00 0
> 754b7855c000-754c9c4bd000 rw-p 00000000 00:00 0
> 754c9d35d000-754ca4000000 rw-p 00000000 00:00 0
> 754ca9e03000-754d6ec7a000 rw-p 00000000 00:00 0
> 754d73a17000-754d88000000 rw-p 00000000 00:00 0
> 754d89f06000-754db2ad8000 rw-p 00000000 00:00 0
> 754db535d000-754dbc000000 rw-p 00000000 00:00 0
> 754dc135d000-754dc8000000 rw-p 00000000 00:00 0
> 754dcdd64000-754e0427c000 rw-p 00000000 00:00 0
> 754e0535d000-754e0c000000 rw-p 00000000 00:00 0
> 754e11bc2000-755030eb2000 rw-p 00000000 00:00 0
> 75503135d000-755038000000 rw-p 00000000 00:00 0
> 75503e7f8000-75504c13e000 rw-p 00000000 00:00 0
> 75504d35d000-755054000000 rw-p 00000000 00:00 0
> 755059a84000-7550d3dfa000 rw-p 00000000 00:00 0
> 7550d535d000-7550dc000000 rw-p 00000000 00:00 0
> 7550e1740000-75512c241000 rw-p 00000000 00:00 0
> 75512d35d000-755134000000 rw-p 00000000 00:00 0
> 755139b87000-755294000000 rw-p 00000000 00:00 0
> 75529ac7a000-75533027c000 rw-p 00000000 00:00 0
> 75533135d000-755338000000 rw-p 00000000 00:00 0
> 75533d35d000-755344000000 rw-p 00000000 00:00 0
> 755344865000-7553e77ad000 rw-p 00000000 00:00 0
> 7553e935d000-7553f0000000 rw-p 00000000 00:00 0
> 7553f50f3000-7554ac624000 rw-p 00000000 00:00 0
> 7554ad35d000-7554b4000000 rw-p 00000000 00:00 0
> 7554b9f6a000-7555ffdfa000 rw-p 00000000 00:00 0
> 7556026ba000-755610000000 rw-p 00000000 00:00 0
> 7556143e3000-755680e13000 rw-p 00000000 00:00 0
> 755683a17000-755698000000 rw-p 00000000 00:00 0
> 75569c09f000-7556d925a000 rw-p 00000000 00:00 0
> 7556d935d000-7556e0000000 rw-p 00000000 00:00 0
> 7556e6ba0000-7557b26ba000 rw-p 00000000 00:00 0
> 7557b8b1c000-755862707000 rw-p 00000000 00:00 0
> 75586535d000-75586c000000 rw-p 00000000 00:00 0
> 75587004d000-755884636000 rw-p 00000000 00:00 0
> 75588535d000-75588c000000 rw-p 00000000 00:00 0
> 755891f7c000-7558dca7d000 rw-p 00000000 00:00 0
>
> Additionally, I get the “WARNING: pixel size (--angpix) is greater than the
>  AutoPick pixel size (--coords_angpix)” prior to loop being performed. I’v
> e ignored this message as advised in other posts. Also, I have bypassed
trai
> ning as my reported values never change during the training or the training
> job never finishes.
>
> Please advise.
>
> Best,
> Jabari
>
>
> ########################################################################
>
> To unsubscribe from the CCPEM list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
>

########################################################################

To unsubscribe from the CCPEM list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
Top of Message | Previous Page | Permalink
JiscMail Tools

Files Area | help
RSS Feeds and Sharing

Search Archives

Advanced Options