New installation of eman2 is not working correctly.

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jm...@psu.edu

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Mar 12, 2018, 6:39:52 PM3/12/18
to EMAN2
Hi
  I just installed a standalone version of EMAN2 from binaries (see below).  All of the tests worked well but as I try to work through my own stained data set as well as the bgal data set I get a number of errors. 

Threadripper 1920x 64GB memory
Ubuntu 16.04
EMAN2.21a download using centos7.sh
I have tried a number of parameters.  This is what happens with 4 threads, but with 1 thread and the standard parameters it falls over on e2simmx with a long list of files then and the hcengine error.

ohnf@Var2CSA:~/Downloads/bgal$ e2projectmanager.py


(python:28911): Gtk-WARNING **: Unable to locate theme engine in module_path: "hcengine",

NOT Writing notes, ppid=-2

Building initial averages

Making subset of ~2000 particles for initial averages

5513 images, processing 0-5512 stepping by 2

2757 images


Classify by k-means

2757 images to classify.

iter 0> 2673 (50)

iter 1> 2659 (50)

iter 2> 2307 (50)

iter 3> 2554 (50)

iter 4> 2306 (50)

iter 5> 2642 (50)

iter 6> 2404 (50)

iter 7> 2449 (50)

iter 8> 2340 (50)

iter 9> 1722 (50)

iter 10> 30 (50)

iter 11> 2484 (50)

iter 12> 2036 (50)

iter 13> 27 (50)

iter 14> 1898 (50)

iter 15> 1850 (50)

iter 16> 1920 (50)

iter 17> 9 (50)

iter 18> 11 (50)

iter 19> 1417 (50)

iter 20> 1422 (50)

iter 21> 1396 (50)

iter 22> 2310 (50)

iter 23> 357 (50)

iter 24> 2161 (50)

iter 25> 17 (50)

iter 26> 16 (50)

iter 27> 2253 (50)

iter 28> 12 (50)

iter 29> 9 (50)

iter 30> 11 (50)

iter 31> 8 (50)

iter 32> 459 (50)

iter 33> 2293 (50)

iter 34> 1479 (50)

iter 35> 9 (50)

iter 36> 10 (50)

iter 37> 9 (50)

iter 38> 2288 (50)

iter 39> 3 (50)

iter 40> 4 (50)

iter 41> 4 (50)

iter 42> 2269 (50)

iter 43> 4 (50)

iter 44> 2 (50)

0) ################################################### (61)

1) ################################################### (61)

2) ######################################################## (67)

3) ########################################## (50)

4) ############################################################# (73)

5) ############################### (37)

6) ######################################### (49)

7) ################################## (41)

8) ################################################################ (76)

9) ########################################################## (69)

10) #################################################### (62)

11) ########################################################### (70)

12) ######################################### (49)

13) ################################################# (59)

14) ####################################################### (66)

15) ################################################## (60)

16) #################################################################### (81)

17) ############################################ (52)

18) ################################################################# (77)

19) ######################################## (48)

20) ############################################# (54)

21) ################################### (42)

22) ################################################## (60)

23) ####################################### (47)

24) ######################################### (49)

25) ####################################################### (65)

26) ####################################### (47)

27) ##################################### (44)

28) ########################### (33)

29) ############################################# (54)

30) ############################################ (52)

31) ########################################## (50)

32) ########################################## (50)

33) ################################# (40)

34) ############################################# (54)

35) ########################################################## (69)

36) ################################################## (60)

37) ########################################### (51)

38) ########################################################### (70)

39) ######################################################################## (85)

40) ############################### (37)

41) ###################################### (45)

42) ############################################################ (72)

43) ####################################################### (65)

44) ########################### (33)

45) ################################# (39)

46) ################################ (38)

47) ########################################### (51)

48) ############################################# (54)

49) ################################# (39)

Class averaging beginning

Error running task : 34

Error running:

e2classaverage.py --input=r2d_02/input_subset.hdf --classmx=r2d_02/classmx_00.hdf --output=r2d_02/classes_init.hdf --iter=8 --force --bootstrap --center=xform.center --align=rotate_translate_tree:maxshift=14 --averager=ctf.weight.autofilt --keep=0.850000 --cmp=ccc --aligncmp=ccc --normproc=normalize.edgemean --parallel=thread:4


Any thoughts?


Steve Ludtke

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Mar 12, 2018, 6:50:18 PM3/12/18
to em...@googlegroups.com
Try switching to the "mean" averager and see if it still crashes. If it does, please provide the exact e2refine2d command-line you ran (from the 'command' tab in e2projectmanager, or from the .eman2log.txt file).   You may also wish to try e2refine2d_bispec instead and see how that works (generally runs faster, and seems to produce superior results).

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)



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JOHN FLANAGAN

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Mar 12, 2018, 6:57:21 PM3/12/18
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Hi
  Ok, I will try that.  Where does one find the .eman2log.txt file?  This should be pretty simple as they are just the downloaded bgal test set so nothing should go wrong correct?


On Mon, Mar 12, 2018 06:50 PM, em...@googlegroups.com wrote:
Try switching to the "mean" averager and see if it still crashes. If it does, please provide the exact e2refine2d command-line you ran (from the 'command' tab in e2projectmanager, or from the .eman2log.txt file).   You may also wish to try e2refine2d_bispec instead and see how that works (generally runs faster, and seems to produce superior results).

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)


On Mar 12, 2018, at 5:39 PM, jm...@psu.edu wrote:

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John M. Flanagan PhD.
Professor
Department of Biochemistry and Molecular Biology
Penn St. College of Medicine
Milton Hershey Medical Center
Hershey PA, 17033



JOHN FLANAGAN

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Mar 12, 2018, 7:00:39 PM3/12/18
to em...@googlegroups.com
Here is with the e2refine2d_bispec

e2refine2d_bispec.py --input=sets/all__ctf_flip_bispec.lst --ncls=32 --iter=3 --nbasisfp=8 --center=xform.center --classkeep=0.8 --classiter=4 --classalign=rotate_translate_tree:flip=0 --classaligncmp=ccc --classraligncmp=ccc --classaverager=ctf.weight.autofilt --classcmp=ccc --classnormproc=normalize.edgemean



(python:32138): Gtk-WARNING **: Unable to locate theme engine in module_path: "hcengine",

NOT Writing notes, ppid=-2

Building initial averages

WARNING: images in sets/all__ctf_flip_bispec.lst have the wrong dimensions. Recomputing bispectra. This will slow processing.


Starting thread 55/56

Classify by k-means

5513 images to classify.

iter 0> 0 (32)

reseed 1 -> 14

reseed 2 -> 5366

reseed 3 -> 2444

reseed 4 -> 2900

reseed 5 -> 1657

reseed 6 -> 1935

reseed 7 -> 2760

reseed 8 -> 479

reseed 9 -> 1477

reseed 10 -> 3382

reseed 11 -> 2132

reseed 12 -> 5022

reseed 13 -> 2543

reseed 14 -> 1069

reseed 15 -> 619

reseed 16 -> 5425

reseed 17 -> 1862

reseed 18 -> 1151

reseed 19 -> 5153

reseed 20 -> 949

reseed 21 -> 2340

reseed 22 -> 3729

reseed 23 -> 1717

reseed 24 -> 4890

reseed 25 -> 846

reseed 26 -> 3541

reseed 27 -> 5007

reseed 28 -> 2261

reseed 29 -> 2545

reseed 30 -> 4157

reseed 31 -> 522

0) ######################################################################## (5513)

1) (1)

2) (1)

3) (1)

4) (1)

5) (1)

6) (1)

7) (1)

8) (1)

9) (1)

10) (1)

11) (1)

12) (1)

13) (1)

14) (1)

15) (1)

16) (1)

17) (1)

18) (1)

19) (1)

20) (1)

21) (1)

22) (1)

23) (1)

24) (1)

25) (1)

26) (1)

27) (1)

28) (1)

29) (1)

30) (1)

31) (1)

Class averaging beginning

InvalidCallException at /home/eman2/anaconda2/conda-bld/eman2_1518620532721/work/libEM/aligner.cpp:2662: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught


Class averaging complete

Input file 'r2db_01/classes_00.hdf' does not exist.

Traceback (most recent call last):

File "/usr/local/bin/EMAN2/bin/e2proc2dpar.py", line 393, in <module>

main()

File "/usr/local/bin/EMAN2/bin/e2proc2dpar.py", line 112, in main

N=EMUtil.get_image_count(args[0])

File "/usr/local/bin/EMAN2/lib/python2.7/site-packages/EMAN2db.py", line 540, in db_get_image_count

raise Exception(fsp)

Exception: r2db_01/classes_00.hdf

Error running:

e2proc2dpar.py r2db_01/classes_00.hdf r2db_01/classes_fp_00.hdf --process math.bispectrum.slice:fp=10:size=32 --threads 4





On Mon, Mar 12, 2018 06:50 PM, em...@googlegroups.com wrote:
Try switching to the "mean" averager and see if it still crashes. If it does, please provide the exact e2refine2d command-line you ran (from the 'command' tab in e2projectmanager, or from the .eman2log.txt file).   You may also wish to try e2refine2d_bispec instead and see how that works (generally runs faster, and seems to produce superior results).

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)


On Mar 12, 2018, at 5:39 PM, jm...@psu.edu wrote:

JOHN FLANAGAN

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Mar 12, 2018, 7:39:28 PM3/12/18
to em...@googlegroups.com

e2refine2d.py --input=sets/all__ctf_flip_lp12.lst --ncls=100 --fastseed --iter=6 --nbasisfp=12 --naliref=5 --center=xform.center --simalign=rotate_translate_tree --simaligncmp=ccc --simraligncmp=dot --simcmp=ccc --classkeep=0.85 --classiter=5 --classalign=rotate_translate_tree --classaligncmp=ccc --classraligncmp=ccc --classaverager=mean --classcmp=ccc --classnormproc=normalize.edgemean


*** Error in `/usr/local/bin/EMAN2/bin/python': double free or corruption (out): 0x000000000727be00 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f891dcf47e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f891dcfd37a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f891dd0153c]
/usr/local/bin/EMAN2/lib/python2.7/site-packages/./libEM2.so(_ZN4EMAN7FactoryINS_9ProcessorEE3getERKSsRKNS_4DictE+0x644)[0x7f891a4f75e4]
/usr/local/bin/EMAN2/lib/python2.7/site-packages/./libEM2.so(_ZNK4EMAN6EMData7processERKSsRKNS_4DictE+0xa9)[0x7f891a4f5739]
/usr/local/bin/EMAN2/lib/python2.7/site-packages/./libEM2.so(_ZNK4EMAN15RT2DTreeAligner17xform_align_nbestEPNS_6EMDataES2_jRKSsRKNS_4DictE+0x2783)[0x7f891a6726d3]
/usr/local/bin/EMAN2/lib/python2.7/site-packages/./libEM2.so(_ZNK4EMAN15RT2DTreeAligner5alignEPNS_6EMDataES2_RKSsRKNS_4DictE+0x55)[0x7f891a659575]
/usr/local/bin/EMAN2/lib/python2.7/site-packages/./libEM2.so(_ZN4EMAN6EMData5alignERKSsPS0_RKNS_4DictES2_S6_+0x10b)[0x7f891a4f5aab]
/usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyEMData2.so(_Z21EMDa! ta_align_wrapper5RN4EMAN6EMDataERKSsPS0_RKNS_4DictES3_S7_+0x43)[0x7f8916a95363]
/usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyEMData2.so(_ZN5boost6python7objects23caller_py_function_implINS0_6detail6callerIPFPN4EMAN6EMDataERS6_RKSsS7_RKNS5_4DictESA_SD_ENS0_19return_value_policyINS0_17manage_new_objectENS0_21default_call_policiesEEENS_3mpl7vector7IS7_S8_SA_S7_SD_SA_SD_EEEEEclEP7_objectSQ_+0x273)[0x7f8916af88e3]
/usr/local/bin/EMAN2/lib/python2.7/site-packages/../../libboost_python.so.1.63.0(_ZNK5boost6python7objects8function4callEP7_objectS4_+0xca)[0x7f891a11b30a]
/usr/local/bin/EMAN2/lib/python2.7/site-packages/../../libboost_python.so.1.63.0(+0x29678)[0x7f891a11b678]
/usr/local/bin/EMAN2/lib/python2.7/site-packages/../../libboost_python.so.1.63.0(_ZN5boost6python21handle_exception_implENS_9function0IvEE+0x53)[0x7f891a1259e3]
/usr/local/bin/EMAN2/lib/python2.7/site-packages/../../libboost_python.so.1.63.0(+0x27f83)[0x7f891a119f83]
/usr/local/bin/EM! AN2/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x53)[0x7f891! e9bde93]
/usr/local/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x715d)[0x7f891ea7080d]
/usr/local/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x89e)[0x7f891ea72c3e]
/usr/local/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x8b47)[0x7f891ea721f7]
/usr/local/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x89e)[0x7f891ea72c3e]
/usr/local/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x8b47)[0x7f891ea721f7]
/usr/local/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x89e)[0x7f891ea72c3e]
/usr/local/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x8b47)[0x7f891ea721f7]
/usr/local/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x89e)[0x7f891ea72c3e]
/usr/local/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x8b47)[0x7f891ea721f7]
/usr/local/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x89e)[0x7f891ea72c3e]
/usr/l! ocal/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x7f891ea72d52]
/usr/local/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(PyRun_FileExFlags+0xb0)[0x7f891ea93450]
/usr/local/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0xef)[0x7f891ea9362f]
/usr/local/bin/EMAN2/bin/../lib/libpython2.7.so.1.0(Py_Main+0xca4)[0x7f891eaa8fd4]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f891dc9d830]
/usr/local/bin/EMAN2/bin/python[0x400729]
======= Memory map: ========
00400000-00401000 r-xp 00000000 103:01 4599090                           /usr/local/bin/EMAN2/bin/python2.7
00600000-00601000 rw-p 00000000 103:01 4599090                           /usr/local/bin/EMAN2/bi! n/python2.7
00a62000-0fa62000 rw-p 00000000 00:00 0  &nbsp! ;                               [heap]
7f88cc000000-7f88cc021000 rw-p 00000000 00:00 0
7f88cc021000-7f88d0000000 ---p 00000000 00:00 0
7f88d3ffd000-7f88d407d000 rw-p 00000000 00:00 0
7f88d407d000-7f88d4082000 r-xp 00000000 103:01 4603897                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/strop.so
7f88d4082000-7f88d4281000 ---p 00005000 103:01 4603897                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/strop.so
7f88d4281000-7f88d4283000 rw-p 00004000 103:01 4603897                   /usr/local/bin/EMAN2/lib/python2.! 7/lib-dynload/strop.so
7f88d4283000-7f88d428b000 r-xp 00000000 103:01 4603860                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_json.so
7f88d428b000-7f88d448b000 ---p 00008000 103:01 4603860                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_json.so
7f88d448b000-7f88d448c000 rw-p 00008000 103:01 4603860                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_json.so
7f88d448c000-7f88d44cc000 rw-p 00000000 00:00 0
7f88d44cc000-7f88d4681000 r-xp 00000000 103:01 4606169                   /usr/local/bin/EMAN2/lib/libdb-5.3.so
7f88d4681000-7f88d4880000 ---p 001b5000 ! 103:01 4606169         &nb! sp;         /usr/local/bin/EMAN2/lib/libdb-5.3.so
7f88d4880000-7f88d488a000 rw-p 001b4000 103:01 4606169                   /usr/local/bin/EMAN2/lib/libdb-5.3.so
7f88d488a000-7f88d48b5000 r-xp 00000000 103:01 4606096                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_bsddb.so
7f88d48b5000-7f88d4ab4000 ---p 0002b000 103:01 4606096                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_bsddb.so
7f88d4ab4000-7f88d4ab8000 rw-p 0002a000 103:01 4606096                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_bsddb.so
7f88d4ab8000-7f88d4ab9! 000 rw-p 00000000 00:00 0
7f88d4ab9000-7f88d4abb000 r-xp 00000000 103:01 4603841                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_bisect.so
7f88d4abb000-7f88d4cba000 ---p 00002000 103:01 4603841                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_bisect.so
7f88d4cba000-7f88d4cbb000 rw-p 00001000 103:01 4603841                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_bisect.so
7f88d4cbb000-7f88d4cc0000 r-xp 00000000 103:01 4473302                   /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f88d4cc0000-7f88d4ebf000 ---p 00005000 103:01 4473302   &nbs! p;           &nb! sp;   /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f88d4ebf000-7f88d4ec0000 r--p 00004000 103:01 4473302                   /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f88d4ec0000-7f88d4ec1000 rw-p 00005000 103:01 4473302                   /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f88d4ec1000-7f88d4ec3000 r-xp 00000000 103:01 4473291                   /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f88d4ec3000-7f88d50c3000 ---p 00002000 103:01 4473291                   /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f88d50c3000-7f88d50c4000 r--p 00002000 103:01 4473291     &nbsp! ;             /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f88d50c4000-7f88d50c5000 rw-p 00003000 103:01 4473291                   /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f88d50c5000-7f88d50d5000 r-xp 00000000 103:01 4473603                   /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f88d50d5000-7f88d52d4000 ---p 00010000 103:01 4473603                   /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f88d52d4000-7f88d52d5000 r--p 0000f000 103:01 4473603                   /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f88d52d5000-7f88d52d6000 rw-p 000100! 00 103:01 4473603         !           /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f88d52d6000-7f88d52db000 r-xp 00000000 103:01 4473342                   /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f88d52db000-7f88d54da000 ---p 00005000 103:01 4473342                   /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f88d54da000-7f88d54db000 r--p 00004000 103:01 4473342                   /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f88d54db000-7f88d54dc000 rw-p 00005000 103:01 4473342                   /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f88d54dc000-7f88d54fd000 r-xp 00000000 ! 103:01 4474709                   /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f88d54fd000-7f88d56fc000 ---p 00021000 103:01 4474709                   /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f88d56fc000-7f88d56fd000 r--p 00020000 103:01 4474709                   /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f88d56fd000-7f88d56fe000 rw-p 00021000 103:01 4474709                   /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f88d56fe000-7f88d5702000 r-xp 00000000 103:01 4474677                   /usr/lib/x86_64-linux-gnu/libxcb-! dri2.so.0.0.0
7f88d5702000-7f88d5901000 ---p 00004000 103:01 4474677!                    /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f88d5901000-7f88d5902000 r--p 00003000 103:01 4474677                   /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f88d5902000-7f88d5903000 rw-p 00004000 103:01 4474677                   /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f88d5903000-7f88d591a000 r-xp 00000000 103:01 4474681                   /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f88d591a000-7f88d5b19000 ---p 00017000 103:01 4474681                   /usr/lib/x86_64-linux-gnu/li! bxcb-glx.so.0.0.0
7f88d5b19000-7f88d5b1b000 r--p 00016000 103:01 4474681                   /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f88d5b1b000-7f88d5b1c000 rw-p 00018000 103:01 4474681                   /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f88d5b1c000-7f88d5c51000 r-xp 00000000 103:01 4473287                   /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f88d5c51000-7f88d5e51000 ---p 00135000 103:01 4473287                   /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f88d5e51000-7f88d5e52000 r--p 00135000 103:01 4473287            &! nbsp;      /usr/lib/x86_64-linux-gnu/libX11.so! .6.3.0
7f88d5e52000-7f88d5e56000 rw-p 00136000 103:01 4473287                   /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f88d5e56000-7f88d5e57000 r-xp 00000000 103:01 4473285                   /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f88d5e57000-7f88d6056000 ---p 00001000 103:01 4473285                   /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f88d6056000-7f88d6057000 r--p 00000000 103:01 4473285                   /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f88d6057000-7f88d6058000 rw-p 00001000 103:01 4473285             &n! bsp;     /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f88d6058000-7f88d605d000 r-xp 00000000 103:01 4473306                   /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f88d605d000-7f88d625c000 ---p 00005000 103:01 4473306                   /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f88d625c000-7f88d625d000 r--p 00004000 103:01 4473306                   /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f88d625d000-7f88d625e000 rw-p 00005000 103:01 4473306                   /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f88d625e000-7f88d6260000 r-xp 00000000 103:01 4473300  !            &nbsp! ;     /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f88d6260000-7f88d645f000 ---p 00002000 103:01 4473300                   /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f88d645f000-7f88d6460000 r--p 00001000 103:01 4473300                   /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f88d6460000-7f88d6461000 rw-p 00002000 103:01 4473300                   /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f88d6461000-7f88d6472000 r-xp 00000000 103:01 4473304                   /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f88d6472000-7f88d6671000 ---p 00011000 103:01 4473304  &n! bsp;                /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f88d6671000-7f88d6672000 r--p 00010000 103:01 4473304                   /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f88d6672000-7f88d6673000 rw-p 00011000 103:01 4473304                   /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f88d6673000-7f88d669d000 r-xp 00000000 103:01 4473804                   /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f88d669d000-7f88d689c000 ---p 0002a000 103:01 4473804                   /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f88d689c! 000-7f88d68a0000 r--p 00029000 103:01 4473804    &n! bsp;              /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f88d68a0000-7f88d68a1000 rw-p 0002d000 103:01 4473804                   /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f88d68a1000-7f88d68a2000 rw-p 00000000 00:00 0
7f88d68a2000-7f88d68a3000 r-xp 00000000 103:01 4474721                   /usr/lib/x86_64-linux-gnu/libxshmfence.so.1.0.0
7f88d68a3000-7f88d6aa3000 ---p 00001000 103:01 4474721                   /usr/lib/x86_64-linux-gnu/libxshmfence.so.1.0.0
7f88d6aa3000-7f88d6aa4000 r--p 00001000 103:01 4474721                   /usr/! lib/x86_64-linux-gnu/libxshmfence.so.1.0.0
7f88d6aa4000-7f88d6aa5000 rw-p 00002000 103:01 4474721                   /usr/lib/x86_64-linux-gnu/libxshmfence.so.1.0.0
7f88d6aa5000-7f88d6aaa000 r-xp 00000000 103:01 4474701                   /usr/lib/x86_64-linux-gnu/libxcb-sync.so.1.0.0
7f88d6aaa000-7f88d6caa000 ---p 00005000 103:01 4474701                   /usr/lib/x86_64-linux-gnu/libxcb-sync.so.1.0.0
7f88d6caa000-7f88d6cab000 r--p 00005000 103:01 4474701                   /usr/lib/x86_64-linux-gnu/libxcb-sync.so.1.0.0
7f88d6cab000-7f88d6cac000 rw-p 00006000 103:01 4474701     &nbsp! ;           &nbs! p; /usr/lib/x86_64-linux-gnu/libxcb-sync.so.1.0.0
7f88d6cac000-7f88d6cae000 r-xp 00000000 103:01 4474689                   /usr/lib/x86_64-linux-gnu/libxcb-present.so.0.0.0
7f88d6cae000-7f88d6ead000 ---p 00002000 103:01 4474689                   /usr/lib/x86_64-linux-gnu/libxcb-present.so.0.0.0
7f88d6ead000-7f88d6eae000 r--p 00001000 103:01 4474689                   /usr/lib/x86_64-linux-gnu/libxcb-present.so.0.0.0
7f88d6eae000-7f88d6eaf000 rw-p 00002000 103:01 4474689                   /usr/lib/x86_64-linux-gnu/libxcb-present.so.0.0.0
7f88d6eaf000-7f88d6eb1000 r-xp 00000000 103:01 4474679  &nbsp! ;                /usr/lib/x86_64-linux-gnu/libxcb-dri3.so.0.0.0
7f88d6eb1000-7f88d70b0000 ---p 00002000 103:01 4474679                   /usr/lib/x86_64-linux-gnu/libxcb-dri3.so.0.0.0
7f88d70b0000-7f88d70b1000 r--p 00001000 103:01 4474679                   /usr/lib/x86_64-linux-gnu/libxcb-dri3.so.0.0.0
7f88d70b1000-7f88d70b2000 rw-p 00002000 103:01 4474679                   /usr/lib/x86_64-linux-gnu/libxcb-dri3.so.0.0.0
7f88d70b2000-7f88d70d8000 r-xp 00000000 103:01 5389062                   /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7! f88d70d8000-7f88d72d8000 ---p 00026000 103:01 5389062   !                 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f88d72d8000-7f88d72da000 r--p 00026000 103:01 5389062                   /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f88d72da000-7f88d72db000 rw-p 00028000 103:01 5389062                   /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f88d72db000-7f88d7349000 r-xp 00000000 103:01 4731478                   /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0
7f88d7349000-7f88d7548000 ---p 0006e000 103:01 4731478                   /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0
7f88d7548000-7f88d! 754b000 r--p 0006d000 103:01 4731478                   /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0
7f88d754b000-7f88d754c000 rw-p 00070000 103:01 4731478                   /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0
7f88d754c000-7f88d754d000 rw-p 00000000 00:00 0
7f88d754d000-7f88d75ba000 r-xp 00000000 103:01 4473147                   /usr/lib/x86_64-linux-gnu/libGLU.so.1.3.1
7f88d75ba000-7f88d77ba000 ---p 0006d000 103:01 4473147                   /usr/lib/x86_64-linux-gnu/libGLU.so.1.3.1
7f88d77ba000-7f88d77bb000 r--p 0006d000 103:01 4473147          !          /usr/lib/x86_64-linux-! gnu/libGLU.so.1.3.1
7f88d77bb000-7f88d77bc000 rw-p 0006e000 103:01 4473147                   /usr/lib/x86_64-linux-gnu/libGLU.so.1.3.1
7f88d77bc000-7f88d77de000 r-xp 00000000 103:01 4607192                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyMarchingCubes2.so
7f88d77de000-7f88d79dd000 ---p 00022000 103:01 4607192                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyMarchingCubes2.so
7f88d79dd000-7f88d79df000 r--p 00021000 103:01 4607192                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyMarchingCubes2.so
7f88d79df000-7f88d79e4000 rw-p 00023000 103! :01 4607192                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyMarchingCubes2.so
7f88d79e4000-7f88d79e5000 rw-p 00000000 00:00 0
7f88d79e5000-7f88d79ef000 r-xp 00000000 103:01 4607135                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyTomoSeg2.so
7f88d79ef000-7f88d7bef000 ---p 0000a000 103:01 4607135                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyTomoSeg2.so
7f88d7bef000-7f88d7bf0000 r--p 0000a000 103:01 4607135                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyTomoSeg2.so
7f88d7bf0000-7f88d7bf1000 rw-p 0000b000 103:0! 1 4607135          &n! bsp;        /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyTomoSeg2.so
7f88d7bf1000-7f88d7c0f000 r-xp 00000000 103:01 4607189                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyAnalyzer2.so
7f88d7c0f000-7f88d7e0e000 ---p 0001e000 103:01 4607189                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyAnalyzer2.so
7f88d7e0e000-7f88d7e10000 r--p 0001d000 103:01 4607189                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyAnalyzer2.so
7f88d7e10000-7f88d7e11000 rw-p 0001f000 103:01 4607189                   /usr/local! /bin/EMAN2/lib/python2.7/site-packages/libpyAnalyzer2.so
7f88d7e11000-7f88d7e22000 r-xp 00000000 103:01 4607170                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyPolarData2.so
7f88d7e22000-7f88d8022000 ---p 00011000 103:01 4607170                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyPolarData2.so
7f88d8022000-7f88d8023000 r--p 00011000 103:01 4607170                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyPolarData2.so
7f88d8023000-7f88d8024000 rw-p 00012000 103:01 4607170                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyPolarData! 2.so
7f88d8024000-7f88d8030000 r-xp 00000000 103:01 4607149 &nb! sp;                 /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyFundamentals2.so
7f88d8030000-7f88d822f000 ---p 0000c000 103:01 4607149                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyFundamentals2.so
7f88d822f000-7f88d8230000 r--p 0000b000 103:01 4607149                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyFundamentals2.so
7f88d8230000-7f88d8231000 rw-p 0000c000 103:01 4607149                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyFundamentals2.so
7f88d8231000-7f88d82b1000 rw-p 00000000 00:00 0
7f88d82e8000-7f88d8309000 r-xp 00000000 103:01 4603! 850                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_ctypes.so
7f88d8309000-7f88d8508000 ---p 00021000 103:01 4603850                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_ctypes.so
7f88d8508000-7f88d850d000 rw-p 00020000 103:01 4603850                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_ctypes.so
7f88d850d000-7f88d854d000 rw-p 00000000 00:00 0
7f88d854d000-7f88d85b5000 r-xp 00000000 103:01 7357218                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/random/mtrand.so
7f88d85b5000-7f88d87b4000 ---p 00068000 103:01 7357218   &nbsp! ;           &nbs! p;   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/random/mtrand.so
7f88d87b4000-7f88d87ed000 rw-p 00067000 103:01 7357218                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/random/mtrand.so
7f88d87ed000-7f88d882e000 rw-p 00000000 00:00 0
7f88d882e000-7f88d8837000 r-xp 00000000 103:01 7225794                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so
7f88d8837000-7f88d8a36000 ---p 00009000 103:01 7225794                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so
7f88d8a36000-7f88d8a37000 rw-p 00008000 103:01 7225794            !        /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so
7f88d8a37000-7f88d8a38000 r-xp 00000000 103:01 4603882                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/future_builtins.so
7f88d8a38000-7f88d8c38000 ---p 00001000 103:01 4603882                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/future_builtins.so
7f88d8c38000-7f88d8c39000 rw-p 00001000 103:01 4603882                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/future_builtins.so
7f88d8c39000-7f88d8c79000 rw-p 00000000 00:00 0
7f88d8c79000-7f88d8c92000 r-xp 00000000 103:01 7357106           &nbsp! ;       /usr/local/bin/EMAN2/lib/python2.! 7/site-packages/numpy/linalg/_umath_linalg.so
7f88d8c92000-7f88d8e91000 ---p 00019000 103:01 7357106                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/linalg/_umath_linalg.so
7f88d8e91000-7f88d8e93000 rw-p 00018000 103:01 7357106                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/linalg/_umath_linalg.so
7f88d8e93000-7f88d8e96000 r-xp 00000000 103:01 7357109                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
7f88d8e96000-7f88d9095000 ---p 00003000 103:01 7357109                   /usr/local/bin/EMAN2/lib/python2.7/site-pac! kages/numpy/linalg/lapack_lite.so
7f88d9095000-7f88d9096000 rw-p 00002000 103:01 7357109                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
7f88d9096000-7f88d909c000 r-xp 00000000 103:01 7357008                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/lib/_compiled_base.so
7f88d909c000-7f88d929c000 ---p 00006000 103:01 7357008                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/lib/_compiled_base.so
7f88d929c000-7f88d929d000 rw-p 00006000 103:01 7357008                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/lib/! _compiled_base.so
7f88d929d000-7f88d92dd000 rw-p 00000000 00:00 0 7f88d92dd000-7f88d92e0000 r-xp 00000000 103:01 4603865                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_random.so
7f88d92e0000-7f88d94df000 ---p 00003000 103:01 4603865                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_random.so
7f88d94df000-7f88d94e0000 rw-p 00002000 103:01 4603865                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_random.so
7f88d94e0000-7f88d94e4000 r-xp 00000000 103:01 4603856                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_hashlib.so
7f88d94e4000-7f88d96e4000 ---p 00004000 103:01 4603856     &nbsp! ;             /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_hashlib.so
7f88d96e4000-7f88d96e5000 rw-p 00004000 103:01 4603856                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_hashlib.so
7f88d96e5000-7f88d9703000 r-xp 00000000 103:01 4603859                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_io.so
7f88d9703000-7f88d9902000 ---p 0001e000 103:01 4603859                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_io.so
7f88d9902000-7f88d990c000 rw-p 0001d000 103:01 4603859                   /usr/local/bin/EMAN2/lib! /python2.7/lib-dynload/_io.so
7f88d990c000-7f88d994c000 rw-p 0000000! 0 00:00 0
7f88d994c000-7f88d994e000 r-xp 00000000 103:01 4603883                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/grp.so
7f88d994e000-7f88d9b4d000 ---p 00002000 103:01 4603883                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/grp.so
7f88d9b4d000-7f88d9b4e000 rw-p 00001000 103:01 4603883                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/grp.so
7f88d9b4e000-7f88d9b8e000 rw-p 00000000 00:00 0
7f88d9b8e000-7f88dbb8e000 rw-p 00000000 00:00 0
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7f88dfb8e000-7f88dfbce000 rw-p 00000000 00:00 0
7f88dfbce000-7f88dfbfb000 r-xp 00000000 103:01 7094445        &nbs! p;          /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/core/scalarmath.so
7f88dfbfb000-7f88dfdfb000 ---p 0002d000 103:01 7094445                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/core/scalarmath.so
7f88dfdfb000-7f88dfdfd000 rw-p 0002d000 103:01 7094445                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/core/scalarmath.so
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7f88ed601000-7f88ede01000 rw-p 00000000 00:00 0
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7f89135d4000-7f8913614000 rw-p 00000000 00:00 0
7f8913614000-7f89136aa000 r-xp 00000000 103:01 4606278                   /usr/local/bin/EMAN2/l! ib/libgfortran.so.1.0.0
7f89136aa000-7f89138a9000 ---p 00096000 103:01 4606278                   /usr/local/bin/EMAN2/lib/libgfortran.so.1.0.0
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7f89138ab000-7f89143ed000 r-xp 00000000 103:01 4606368                   /usr/local/bin/EMAN2/lib/libopenblas_nehalemp-r0.2.14.so
7f89143ed000-7f89145ec000 ---p 00b42000 103:01 4606368                   /usr/local/bin/EMAN2/lib/libopenblas_nehalemp-r0.2.14.so
7f89145ec000-7f89145fb000 rw-p 00b41000 103:01 4606368      &! nbsp;           ! /usr/local/bin/EMAN2/lib/libopenblas_nehalemp-r0.2.14.so
7f89145fb000-7f8914712000 rw-p 00000000 00:00 0
7f8914712000-7f8914718000 r-xp 00000000 103:01 7094377                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/core/_dotblas.so
7f8914718000-7f8914917000 ---p 00006000 103:01 7094377                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/core/_dotblas.so
7f8914917000-7f8914918000 rw-p 00005000 103:01 7094377                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/core/_dotblas.so
7f8914918000-7f891491b000 r-xp 00000000 103:01 4603857                 &nbsp! ; /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_heapq.so
7f891491b000-7f8914b1b000 ---p 00003000 103:01 4603857                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_heapq.so
7f8914b1b000-7f8914b1d000 rw-p 00003000 103:01 4603857                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_heapq.so
7f8914b1d000-7f8914b27000 r-xp 00000000 103:01 4603884                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/itertools.so
7f8914b27000-7f8914d27000 ---p 0000a000 103:01 4603884                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/itertools.so
7f8914d27000-7f8914d2c000 rw! -p 0000a000 103:01 4603884       &nb! sp;           /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/itertools.so
7f8914d2c000-7f8914d34000 r-xp 00000000 103:01 4603889                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/operator.so
7f8914d34000-7f8914f34000 ---p 00008000 103:01 4603889                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/operator.so
7f8914f34000-7f8914f36000 rw-p 00008000 103:01 4603889                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/operator.so
7f8914f36000-7f8914f3d000 r-xp 00000000 103:01 4603848                   /usr/local/bin/EMAN2/li! b/python2.7/lib-dynload/_collections.so
7f8914f3d000-7f891513c000 ---p 00007000 103:01 4603848                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_collections.so
7f891513c000-7f891513e000 rw-p 00006000 103:01 4603848                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/_collections.so
7f891513e000-7f89151ac000 r-xp 00000000 103:01 7094526                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/core/umath.so
7f89151ac000-7f89153ac000 ---p 0006e000 103:01 7094526                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/core/umath.so
7f89153ac000-7f89! 153b1000 rw-p 0006e000 103:01 7094526     &nbs! p;             /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/core/umath.so
7f89153b1000-7f89153b3000 rw-p 00000000 00:00 0
7f89153b3000-7f89153c5000 r-xp 00000000 103:01 4603880                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/datetime.so
7f89153c5000-7f89155c4000 ---p 00012000 103:01 4603880                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/datetime.so
7f89155c4000-7f89155c8000 rw-p 00011000 103:01 4603880                   /usr/local/bin/EMAN2/lib/python2.7/lib-dynload/datetime.so
7f89155c8000-7f891575f000 r-xp 00000000 103:01 7094436          !          /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/core/multiarray.so
7f891575f000-7f891595f000 ---p 00197000 103:01 7094436                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/core/multiarray.so
7f891595f000-7f891596e000 rw-p 00197000 103:01 7094436                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/numpy/core/multiarray.so
7f891596e000-7f891597f000 rw-p 00000000 00:00 0
7f891597f000-7f89159b1000 r-xp 00000000 103:01 4607198                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyTypeConverter2.so
7f89159b1000-7f8915bb0000 ---p 00032000 103:01 4607198      &n! bsp;            ! /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyTypeConverter2.so
7f8915bb0000-7f8915bb2000 r--p 00031000 103:01 4607198                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyTypeConverter2.so
7f8915bb2000-7f8915bb3000 rw-p 00033000 103:01 4607198                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyTypeConverter2.so
7f8915bb3000-7f8915bca000 r-xp 00000000 103:01 4607183                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyPDBReader2.so
7f8915bca000-7f8915dca000 ---p 00017000 103:01 4607183                   /usr/local/bin/EMAN2/lib/python2.7/site-! packages/libpyPDBReader2.so
7f8915dca000-7f8915dcb000 r--p 00017000 103:01 4607183                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyPDBReader2.so
7f8915dcb000-7f8915dcc000 rw-p 00018000 103:01 4607183                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyPDBReader2.so
7f8915dcc000-7f8915e0a000 r-xp 00000000 103:01 4607206                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyPointArray2.so
7f8915e0a000-7f891600a000 ---p 0003e000 103:01 4607206                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyPointArray2.so
7f891600a000-7f8916! 00d000 r--p 0003e000 103:01 4607206      !              /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyPointArray2.so
7f891600d000-7f891600f000 rw-p 00041000 103:01 4607206                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyPointArray2.so
7f891600f000-7f89161e0000 r-xp 00000000 103:01 4607215                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyUtils2.so
7f89161e0000-7f89163df000 ---p 001d1000 103:01 4607215                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyUtils2.so
7f89163df000-7f89163eb000 r--p 001d0000 103:01 4607215               &nbs! p;   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyUtils2.so
7f89163eb000-7f89163ee000 rw-p 001dc000 103:01 4607215                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyUtils2.so
7f89163ee000-7f89164bb000 rw-p 00000000 00:00 0
7f89164bb000-7f8916599000 r-xp 00000000 103:01 4607213                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyTransform2.so
7f8916599000-7f8916798000 ---p 000de000 103:01 4607213                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyTransform2.so
7f8916798000-7f891679f000 r--p 000dd000 103:01 4607213                 !   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyTransform2! .so
7f891679f000-7f89167a3000 rw-p 000e4000 103:01 4607213                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyTransform2.so
7f89167a3000-7f89167a5000 rw-p 00000000 00:00 0
7f89167a5000-7f89167d3000 r-xp 00000000 103:01 4607199                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyGeometry2.so
7f89167d3000-7f89169d2000 ---p 0002e000 103:01 4607199                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyGeometry2.so
7f89169d2000-7f89169d4000 r--p 0002d000 103:01 4607199                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyGeometry2.so!
7f89169d4000-7f89169d5000 rw-p 0002f000 103:01 4607199                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyGeometry2.so
7f89169d5000-7f89169d6000 rw-p 00000000 00:00 0
7f89169d6000-7f8916b41000 r-xp 00000000 103:01 4607214                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyEMData2.so
7f8916b41000-7f8916d41000 ---p 0016b000 103:01 4607214                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyEMData2.so
7f8916d41000-7f8916d4a000 r--p 0016b000 103:01 4607214                   /usr/local/bin/EMAN2/lib/python2.7/site-packages/libpyEMData2.so


On! Mon, Mar 12, 2018 06:50 PM, em...@googlegroups.com wrote:
Try switching to the "mean" averager and see if it still crashes. If it does, please provide the exact e2refine2d command-line you ran (from the 'command' tab in e2projectmanager, or from the .eman2log.txt file).   You may also wish to try e2refine2d_bispec instead and see how that works (generally runs faster, and seems to produce superior results).

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)


On Mar 12, 2018, at 5:39 PM, jm...@psu.edu wrote:

Steve Ludtke

unread,
Mar 12, 2018, 7:42:07 PM3/12/18
to em...@googlegroups.com
Hmm,

1) looks like you may have started processing with an older snapshot of EMAN2?  If you see this:

WARNING: images in sets/all__ctf_flip_bispec.lst have the wrong dimensions. Recomputing bispectra. This will slow processing.


it implies you should rerun CTF autoprocessing, optionally with the "--outputonly" option (for speed)

2) something else funny seems to be going on. Can you tell me what box size you used when picking particles?  Use the browser (e2display.py) and have a look in particles/ and see what dimensions the _fullres particles have...

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)


JOHN FLANAGAN

unread,
Mar 13, 2018, 9:58:47 AM3/13/18
to em...@googlegroups.com
Hi
  I did realize on the first one that the box size was too small.  I just imported the boxes from the test set without looking as I was trying to test the program rather than do the refinement per se.  I will look to see what is going on there, I thought that I fixed that in the next round of extractions, but perhaps not.

Cheers
John


On Mon, Mar 12, 2018 07:42 PM, em...@googlegroups.com wrote:
Hmm,

1) looks like you may have started processing with an older snapshot of EMAN2?  If you see this:

WARNING: images in sets/all__ctf_flip_bispec.lst have the wrong dimensions. Recomputing bispectra. This will slow processing.


it implies you should rerun CTF autoprocessing, optionally with the "--outputonly" option (for speed)
2) something else funny seems to be going on. Can you tell me what box size you used when picking particles?  Use the browser (e2display.py) and have a look in particles/ and see what dimensions the _fullres particles have...
--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)


On Mar 12, 2018, at 6:00 PM, JOHN FLANAGAN <jm...@psu.edu> wrote:

Groups "EMAN2" group.
To post to this group, send email to eman2@go! oglegroups.com

JOHN FLANAGAN

unread,
Mar 13, 2018, 11:02:37 AM3/13/18
to em...@googlegroups.com
Hi
  I got same error with a box size of 288 (which from my reading is a good box size) but the bispec had dimensions of 16x320x1.  The all.lst 288x288, fullres 288x288 lp12 96x96 and lp5 180x180.  As I have never used the bispectrum I am unclear as to the appropriate value for this box size.


Cheers
John


On Mon, Mar 12, 2018 07:42 PM, em...@googlegroups.com wrote:
Hmm,

1) looks like you may have started processing with an older snapshot of EMAN2?  If you see this:

WARNING: images in sets/all__ctf_flip_bispec.lst have the wrong dimensions. Recomputing bispectra. This will slow processing.


it implies you should rerun CTF autoprocessing, optionally with the "--outputonly" option (for speed)
2) something else funny seems to be going on. Can you tell me what box size you used when picking particles?  Use the browser (e2display.py) and have a look in particles/ and see what dimensions the _fullres particles have...
--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)


On Mar 12, 2018, at 6:00 PM, JOHN FLANAGAN <jm...@psu.edu> wrote:

Groups "EMAN2" group.
To post to this group, send email to eman2@go! oglegroups.com

JOHN FLANAGAN

unread,
Mar 13, 2018, 11:03:51 AM3/13/18
to em...@googlegroups.com
When using the --outputonly option i got Rubbish!! Option 'outputonly' not found.


On Mon, Mar 12, 2018 07:42 PM, em...@googlegroups.com wrote:
Hmm,

1) looks like you may have started processing with an older snapshot of EMAN2?  If you see this:

WARNING: images in sets/all__ctf_flip_bispec.lst have the wrong dimensions. Recomputing bispectra. This will slow processing.


it implies you should rerun CTF autoprocessing, optionally with the "--outputonly" option (for speed)
2) something else funny seems to be going on. Can you tell me what box size you used when picking particles?  Use the browser (e2display.py) and have a look in particles/ and see what dimensions the _fullres particles have...
--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)


On Mar 12, 2018, at 6:00 PM, JOHN FLANAGAN <jm...@psu.edu> wrote:

Groups "EMAN2" group.
To post to this group, send email to eman2@go! oglegroups.com

Steve Ludtke

unread,
Mar 13, 2018, 11:13:39 AM3/13/18
to em...@googlegroups.com
You gave that option to e2ctf_auto ?  I'm a little unclear as to the sequence you've followed now:

- 288 is a reasonable box size, yes
- bispectra are all 16x320 or 34x32x10, so sounds also fine
- if --outputonly gives you problems, you can rerun e2ctf_auto without that option, it will take a little longer, but not so terribly much
- if you get a crash in 2D or 3D refinement, please try switching to the "mean" averager and try again. If this solves the problem, it implies something is severely messed up in your CTF parameters, and you should check the fitting with the interactive interface (the tutorial describes this).

If it's still crashing, then please report again, and we can dig a little deeper.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)


JOHN FLANAGAN

unread,
Mar 13, 2018, 3:39:35 PM3/13/18
to em...@googlegroups.com
Steve,
  I have gotten things to run RFCA and using mean have not gone back to try the default.  This worked pretty well.  On the other hand I still do cannot get the Bispectrum-based class averages to work (did not use mean though).  The error is still size error on the front end (16x320).  I did look at the CTF corrections and they look ok, as they should since this is the bgal test set and should breeze through them with minimal problem.  Any thoughts as to why the bispectrum is throwing this warning?


On Tue, Mar 13, 2018 11:13 AM, em...@googlegroups.com wrote:
You gave that option to e2ctf_auto ?  I'm a little unclear as to the sequence you've followed now:

- 288 is a reasonable box size, yes
- bispectra are all 16x320 or 34x32x10, so sounds also fine
- if --outputonly gives you problems, you can rerun e2ctf_auto without that option, it will take a little longer, but not so terribly much
- if you get a crash in 2D or 3D refinement, please try switching to the "mean" averager and try again. If this solves the problem, it implies something is severely messed up in your CTF parameters, and you should check the fitting with the interactive interface (the tutorial describes this).

If it's still crashing, then please report again, and we can dig a little deeper.
--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)


On Mar 13, 2018, at 10:03 AM, JOHN FLANAGAN <jm...@psu.edu> wrote:

Groups "EMAN2" group.
To post to this group, send email to eman2@! go! oglegroups.com

JOHN FLANAGAN

unread,
Mar 13, 2018, 3:40:39 PM3/13/18
to em...@googlegroups.com
Also bispectrum still falls over with standard parameters.


On Tue, Mar 13, 2018 11:13 AM, em...@googlegroups.com wrote:
You gave that option to e2ctf_auto ?  I'm a little unclear as to the sequence you've followed now:

- 288 is a reasonable box size, yes
- bispectra are all 16x320 or 34x32x10, so sounds also fine
- if --outputonly gives you problems, you can rerun e2ctf_auto without that option, it will take a little longer, but not so terribly much
- if you get a crash in 2D or 3D refinement, please try switching to the "mean" averager and try again. If this solves the problem, it implies something is severely messed up in your CTF parameters, and you should check the fitting with the interactive interface (the tutorial describes this).

If it's still crashing, then please report again, and we can dig a little deeper.
--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)


On Mar 13, 2018, at 10:03 AM, JOHN FLANAGAN <jm...@psu.edu> wrote:

Groups "EMAN2" group.
To post to this group, send email to eman2@! go! oglegroups.com

JOHN FLANAGAN

unread,
Mar 14, 2018, 12:06:55 PM3/14/18
to em...@googlegroups.com
Hi Steve
  The Reference free Class averaging works like a charm with default parameters.  However, the Bispectrum-based CA does not work even with mean (i.e. likely not the CTF correction and I checked all of them and they are pretty good).  The error is as before

Still throws an image is the wrong size despite being 16 320 and then says that needs even number during averaging resulting in a fail.

Sorry to bother you but I am trying to get things running stably as possible.

e2refine2d_bispec.py --input=sets/all__ctf_flip_bispec.lst --ncls=64 --iter=3 --nbasisfp=8 --parallel=thread:16 --center=xform.center --classkeep=0.8 --classiter=4 --classalign=rotate_translate_tree:flip=0 --classaligncmp=ccc --classraligncmp=ccc --classaverager=ctf.weight.autofilt --classcmp=ccc --classnormproc=normalize.edgemean


NOT Writing notes, ppid=-2

--threads set to match --parallel

Building initial averages

WARNING: images in sets/all__ctf_flip_bispec.lst have the wrong dimensions. Recomputing bispectra. This will slow processing.

Starting thread 101/102

Classify by k-means

10118 images to classify.

iter 0> 0 (64)

reseed 1 -> 4056

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0) ######################################################################## (10118)

32) (1)

33) (1)

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63) (1)

Class averaging beginning

InvalidCallException at /home/eman2/anaconda2/conda-bld/eman2_1518620532721/work/libEM/aligner.cpp:2662: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught


Class averaging complete

Cleaning up thread server. Please wait.

Input file 'r2db_01/classes_00.hdf' does not exist.

Traceback (most recent call last):

File "/usr/local/bin/EMAN2/bin/e2proc2dpar.py", line 393, in <module>

main()

File "/usr/local/bin/EMAN2/bin/e2proc2dpar.py", line 112, in main

N=EMUtil.get_image_count(args[0])

File "/usr/local/bin/EMAN2/lib/python2.7/site-packages/EMAN2db.py", line 540, in db_get_image_count

raise Exception(fsp)

Exception: r2db_01/classes_00.hdf

Error running:

e2proc2dpar.py r2db_01/classes_00.hdf r2db_01/classes_fp_00.hdf --process math.bispectrum.slice:fp=10:size=32 --threads 16




On Tue, Mar 13, 2018 11:13 AM, em...@googlegroups.com wrote:
You gave that option to e2ctf_auto ?  I'm a little unclear as to the sequence you've followed now:

- 288 is a reasonable box size, yes
- bispectra are all 16x320 or 34x32x10, so sounds also fine
- if --outputonly gives you problems, you can rerun e2ctf_auto without that option, it will take a little longer, but not so terribly much
- if you get a crash in 2D or 3D refinement, please try switching to the "mean" averager and try again. If this solves the problem, it implies something is severely messed up in your CTF parameters, and you should check the fitting with the interactive interface (the tutorial describes this).

If it's still crashing, then please report again, and we can dig a little deeper.
--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)


On Mar 13, 2018, at 10:03 AM, JOHN FLANAGAN <jm...@psu.edu> wrote:

Groups "EMAN2" group.
To post to this group, send email to eman2@! go! oglegroups.com

Steve Ludtke

unread,
Mar 15, 2018, 11:47:12 PM3/15/18
to em...@googlegroups.com
Hi John,
sorry, was traveling without laptop. You aren't supposed to directly specify the _bispec data. The input file for e2refine2d_bispec is normally the _fullres set. The _bispec set is used automatically, you never specify it. The only reason it exists explicitly at all is because it takes a lot of CPU time to compute.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)


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