Appion

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...