sprint python error: TypeError: unsupported operand type(s) for +: 'NoneType' and 'NoneType'
cisb...@gmail.com
Does anybody have any idea what the below python error means please ?
spring --version && springenv e2version.py
Spring environment loaded.
GUI from package Emspring-0.83.1449
Spring environment loaded.
EMAN 2.1 alpha2 (CVS 2013/08/07 17:01:09)
Your EMAN2 is running on: Red Hat Enterprise Linux Workstation release 6.2 (Santiago)
Red Hat Enterprise Linux Workstation release 6.2 (Santiago) 2.6.32-220.el6.x86_64 x86_64
Your Python version is: 2.7.2
ERROR:
Traceback (most recent call last):
File "/src/spring/spring_v0-83-1449/bin/segmentexam_mpi", line 137, in <module>
sys.exit(spring.segment2d.segmentexam_mpi.main())
File "/src/spring/spring_v0-83-1449/lib/python2.7/site-packages/emspring-0.83.1449-py2.7.egg/spring/segment2d/segmentexam_mpi.py", line 175, in main
stack.add_up_power_spectra()
File "/src/spring/spring_v0-83-1449/lib/python2.7/site-packages/emspring-0.83.1449-py2.7.egg/spring/segment2d/segmentexam_mpi.py", line 158, in add_up_power_spectra
self.correlate_layer_line_region_mpi(segment_ids, avg_periodogram, power_infilestack)
File "/src/spring/spring_v0-83-1449/lib/python2.7/site-packages/emspring-0.83.1449-py2.7.egg/spring/segment2d/segmentexam_mpi.py", line 120, in correlate_layer_line_region_mpi
self.enter_correlation_values_in_database(correlations, segment_ids)
File "/src/spring/spring_v0-83-1449/lib/python2.7/site-packages/emspring-0.83.1449-py2.7.egg/spring/segment2d/segmentexam.py", line 813, in enter_correlation_values_in_database
avg_ccc_layer = np.mean([each_cc for each_cc in cc_per_helix])
File "/src/spring/spring_v0-83-1449/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2727, in mean
out=out, keepdims=keepdims)
File "/src/spring/spring_v0-83-1449/lib/python2.7/site-packages/numpy/core/_methods.py", line 66, in _mean
ret = umr_sum(arr, axis, dtype, out, keepdims)
TypeError: unsupported operand type(s) for +: 'NoneType' and 'NoneType'
Thank you
Dr Suhail A Islam
Imperial College London
Carsten Sachse
cisb...@gmail.com
Thank you for your reply. Here is further information:
The program used was segmentexam and the parameters together with the output error messages follow:
segmentexam --f segmentexam_22_Apr_2015_17_28_23_9374.par
Spring environment loaded.
****************************************************************************
* Hwloc has encountered what looks like an error from the operating system.
*
* object intersection without inclusion!
* Error occurred in topology.c line 594
*
* Please report this error message to the hwloc user's mailing list,
* along with the output from the hwloc-gather-topology.sh script.
****************************************************************************
****************************************************************************
* Hwloc has encountered what looks like an error from the operating system.
*
* object intersection without inclusion!
* Error occurred in topology.c line 594
*
* Please report this error message to the hwloc user's mailing list,
* along with the output from the hwloc-gather-topology.sh script.
****************************************************************************
Program to examine all excised in-plane rotated segments and compute their collapsed (1D) and
2D power spectrum and width profile of helices
Input parameters are read from segmentexam_22_Apr_2015_17_28_23_9374.par
The following input parameters have been received:
Image input stack = /exports/csb/csb/home/segment_31_Mar_2015_13_30_05_45620/SPRING_sk_COMPLETE_4class.hdf
Diagnostic plot = SPRING_sk_COMPLETE_4class_segexam_085_BEST_Width_CC.pdf
Power spectrum output image = SPRING_sk_COMPLETE_4class_pow_085_BEST_Width_CC.hdf
Enhanced power spectrum option = True
Enhanced power spectrum output image = SPRING_sk_COMPLETE_4class_Epow_085_BEST_Width_CC.hdf
Pixel size in Angstrom = 1.03
Estimated helix width in Angstrom = 350
Power spectrum resolution cutoff in 1/Angstrom = 0.1
Compute layer-line correlation option = True
Layer-line region in 1/Angstrom = (0.001, 0.08)
Reference power spectrum = True
Power spectrum input image = /exports/csb/csb/home/segmentexam_14_Apr_2015_18_16_59_9374/SPRING_sk_COMPLETE_4class_pow_CC_085_BEST50percent.hdf
spring.db file = /exports/csb/csb/home/segment_31_Mar_2015_13_30_05_45620/spring.db
Micrographs select option = True
Include or exclude micrographs = include
Micrographs list = 85
Helices select option = False
Include or exclude helices = include
Helices list =
Segments select option = False
Include or exclude segments = include
Segment file = /exports/csb/csb/home/Width_10A.dat
Classes select option = False
Include or exclude classes = include
Class type = class_id
Classes list =
Persistence class option = False
Persistence class length in Angstrom = 1
Class occupancy threshold = 0.0
Straightness select option = False
Include or exclude straight helices = include
Persistence length range = (0, 0)
Layer line correlation select option = False
Include or exclude segments based on layer-line correlation = include
Correlation layer line range = (0, 0)
Defocus select option = False
Include or exclude defocus range = include
Defocus range = (0, 0)
Astigmatism select option = False
Include or exclude astigmatic segments = include
Astigmatism range = (0, 0)
MPI option = True
Number of CPUs = 8
Temporary directory = /exports/csb/csb/home/
/exports/csb/csb/home/segment_31_Mar_2015_13_30_05_45620/SPRING_sk_COMPLETE_4class.hdf found
/exports/csb/csb/home/segmentexam_14_Apr_2015_18_16_59_9374/SPRING_sk_COMPLETE_4class_pow_CC_085_BEST50percent.hdf found
/exports/csb/csb/home/segment_31_Mar_2015_13_30_05_45620/spring.db found
/exports/csb/csb/home/ found
****************************************************************************
* Hwloc has encountered what looks like an error from the operating system.
*
* object intersection without inclusion!
* Error occurred in topology.c line 594
*
* Please report this error message to the hwloc user's mailing list,
* along with the output from the hwloc-gather-topology.sh script.
****************************************************************************
Program to examine all excised in-plane rotated segments and compute their collapsed (1D) and
2D power spectrum and width profile of helices
Input parameters are read from parfile_63065.par
The following input parameters have been received:
Image input stack = /exports/csb/csb/home/segment_31_Mar_2015_13_30_05_45620/SPRING_sk_COMPLETE_4class.hdf
Diagnostic plot = SPRING_sk_COMPLETE_4class_segexam_085_BEST_Width_CC.pdf
Power spectrum output image = SPRING_sk_COMPLETE_4class_pow_085_BEST_Width_CC.hdf
Enhanced power spectrum option = True
Enhanced power spectrum output image = SPRING_sk_COMPLETE_4class_Epow_085_BEST_Width_CC.hdf
Pixel size in Angstrom = 1.03
Estimated helix width in Angstrom = 350
Power spectrum resolution cutoff in 1/Angstrom = 0.1
Compute layer-line correlation option = True
Layer-line region in 1/Angstrom = (0.001, 0.08)
Reference power spectrum = True
Power spectrum input image = /exports/csb/csb/home/segmentexam_14_Apr_2015_18_16_59_9374/SPRING_sk_COMPLETE_4class_pow_CC_085_BEST50percent.hdf
spring.db file = /exports/csb/csb/home/segment_31_Mar_2015_13_30_05_45620/spring.db
Micrographs select option = True
Include or exclude micrographs = include
Micrographs list = 85
Helices select option = False
Include or exclude helices = include
Helices list =
Segments select option = False
Include or exclude segments = include
Segment file = /exports/csb/csb/home/Width_10A.dat
Classes select option = False
Include or exclude classes = include
Class type = class_id
Classes list =
Persistence class option = False
Persistence class length in Angstrom = 1
Class occupancy threshold = 0.0
Straightness select option = False
Include or exclude straight helices = include
Persistence length range = (0, 0)
Layer line correlation select option = False
Include or exclude segments based on layer-line correlation = include
Correlation layer line range = (0, 0)
Defocus select option = False
Include or exclude defocus range = include
Defocus range = (0, 0)
Astigmatism select option = False
Include or exclude astigmatic segments = include
Astigmatism range = (0, 0)
MPI option = True
Number of CPUs = 8
Temporary directory = /exports/csb/csb/home/
/exports/csb/csb/home/segment_31_Mar_2015_13_30_05_45620/SPRING_sk_COMPLETE_4class.hdf found
/exports/csb/csb/home/segmentexam_14_Apr_2015_18_16_59_9374/SPRING_sk_COMPLETE_4class_pow_CC_085_BEST50percent.hdf found
/exports/csb/csb/home/segment_31_Mar_2015_13_30_05_45620/spring.db found
/exports/csb/csb/home/ found
Traceback (most recent call last):
File "/exports/csb/csb/soft/Linux64/src/spring/spring_v0-83-1449/bin/segmentexam_mpi", line 137, in <module>
sys.exit(spring.segment2d.segmentexam_mpi.main())
File "/exports/csb/csb/soft/Linux64/src/spring/spring_v0-83-1449/lib/python2.7/site-packages/emspring-0.83.1449-py2.7.egg/spring/segment2d/segmentexam_mpi.py", line 175, in main
stack.add_up_power_spectra()
File "/exports/csb/csb/soft/Linux64/src/spring/spring_v0-83-1449/lib/python2.7/site-packages/emspring-0.83.1449-py2.7.egg/spring/segment2d/segmentexam_mpi.py", line 158, in add_up_power_spectra
self.correlate_layer_line_region_mpi(segment_ids, avg_periodogram, power_infilestack)
File "/exports/csb/csb/soft/Linux64/src/spring/spring_v0-83-1449/lib/python2.7/site-packages/emspring-0.83.1449-py2.7.egg/spring/segment2d/segmentexam_mpi.py", line 120, in correlate_layer_line_region_mpi
self.enter_correlation_values_in_database(correlations, segment_ids)
File "/exports/csb/csb/soft/Linux64/src/spring/spring_v0-83-1449/lib/python2.7/site-packages/emspring-0.83.1449-py2.7.egg/spring/segment2d/segmentexam.py", line 813, in enter_correlation_values_in_database
avg_ccc_layer = np.mean([each_cc for each_cc in cc_per_helix])
File "/exports/csb/csb/soft/Linux64/src/spring/spring_v0-83-1449/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2727, in mean
out=out, keepdims=keepdims)
File "/exports/csb/csb/soft/Linux64/src/spring/spring_v0-83-1449/lib/python2.7/site-packages/numpy/core/_methods.py", line 66, in _mean
ret = umr_sum(arr, axis, dtype, out, keepdims)
TypeError: unsupported operand type(s) for +: 'NoneType' and 'NoneType'
Rank 0 on machine csbserv1 with process ID 63072 raised an error message. Find the corresponding error message above. All other MPI processes are aborted. Ignore the error messages thereafter as they can arise as a result of the aborting procedure.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 63072 on
node csbserv1 exiting improperly. There are two reasons this could occur:
1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.
2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"
This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
****************************************************************************
* Hwloc has encountered what looks like an error from the operating system.
*
* object intersection without inclusion!
* Error occurred in topology.c line 594
*
* Please report this error message to the hwloc user's mailing list,
* along with the output from the hwloc-gather-topology.sh script.
****************************************************************************
The following temporary directories were cleared and removed:
rank host process_id temporary directory
------ -------- ------------ --------------------------------------------------------------------------------------------------------
0 csbserv1 63072 /exports/csb/csb/home/22_Apr_2015_17_53_39-63072/
1 csbserv1 63073 /exports/csb/csb/home/22_Apr_2015_17_53_39-63073/
2 csbserv1 63074 /exports/csb/csb/home/22_Apr_2015_17_53_39-63074/
3 csbserv1 63075 /exports/csb/csb/home/22_Apr_2015_17_53_39-63075/
4 csbserv1 63076 /exports/csb/csb/home/22_Apr_2015_17_53_39-63076/
5 csbserv1 63077 /exports/csb/csb/home/22_Apr_2015_17_53_39-63077/
6 csbserv1 63078 /exports/csb/csb/home/22_Apr_2015_17_53_39-63078/
7 csbserv1 63079 /exports/csb/csb/home/22_Apr_2015_17_53_39-63079/
Carsten Sachse
...
cisb...@gmail.com
The user tried this and reports that he is still getting the same error.
Regards
suhail