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Bug #4598
openError creating stack on SEMC cluster
Status:
New
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Start date:
11/15/2016
Due date:
% Done:
0%
Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:
Description
Runtime error when trying to create a stack by command line or through Appion on SEMC cluster. Same stack creation worked on guppy.
Command:
/opt/myamisnap/bin/appion makestack2.py --single=start.hed --selectionid=6 --invert --normalize-method=edgenorm --phaseflip --flip-type=ace2imagephase --sort-type=res80 --boxsize=112 --bin=2 --filetype=imagic --forceInsert --description="manualmasker 3 112 bin 2 phaseflip" --runname=stack00 --rundir=/gpfs/appion/araczkowski/rjain/16oct20i/stacks/stack00 --preset=en --commit --projectid=165 --session=16oct20i --no-rejects --no-wait --continue --expid=2802 --jobtype=makestack2
Output:
RuntimeError: module compiled against API version 6 but this version of numpy is 4 RuntimeError: module compiled against API version 6 but this version of numpy is 4 Warning! ***HDF5 library version mismatched error*** The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a different version of static or shared HDF5 library. You should recompile the application or check your shared library related settings such as 'LD_LIBRARY_PATH'. You can, at your own risk, disable this warning by setting the environment variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. Setting it to 2 or higher will suppress the warning messages totally. Headers are 1.8.5, library is 1.8.6 SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.8.6 Configured on: Fri Oct 28 07:35:10 EDT 2011 Configured by: batserve@bat4216glnxa64 at The MathWorks, Inc., Natick, MA 01760 Configure mode: production Host system: x86_64-unknown-linux-gnu Uname information: Linux bat4216glnxa64 2.6.32-5-amd64 #1 SMP Mon Mar 7 21:35:22 UTC 2011 x86_64 GNU/Linux Byte sex: little-endian Libraries: Installation point: /mathworks/BLR/devel/bat/A3p1/build/3p/install/318546/glnxa64/hdf5 Compiling Options: ------------------ Compilation Mode: production C Compiler: /mathworks/hub/3rdparty/internal/301231/glnxa64/gcc-4.4.6/bin/gcc ( gcc (GCC) 4.4.6) CFLAGS: -O2 -pipe -pthread -fPIC H5_CFLAGS: -ansi -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -O3 -fomit-frame-pointer -finline-functions AM_CFLAGS: CPPFLAGS: H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE Shared Libraries: yes Static Libraries: no Statically Linked Executables: no LDFLAGS: -pthread AM_LDFLAGS: Extra libraries: -lz -lm Archiver: ar Ranlib: ranlib Debugged Packages: API Tracing: no Languages: ---------- Fortran: no C++: no Features: --------- Parallel HDF5: no High Level library: yes Threadsafety: no Default API Mapping: v18 With Deprecated Public Symbols: yes I/O filters (external): deflate(zlib) I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset MPE: no Direct VFD: no dmalloc: no Clear file buffers before write: yes Using memory checker: no Function Stack Tracing: no GPFS: no Strict File Format Checks: no Optimization Instrumentation: no Large File Support (LFS): yes H5dump Packed Bits: yes Bye...
Updated by Anchi Cheng almost 8 years ago
Sorry my bad. Forgot to keep the special change intact in myami-beta when I update. Fixed now.
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