Error Detected In Hdf5 1.8.4-patch1
Sign in Pricing Blog Support Search GitHub This repository Watch 31 Star 146 Fork 108 CellProfiler/CellProfiler Code Issues 273 Pull requests 31 Projects 7 Wiki Pulse Graphs New issue HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread #1565 Closed 0x00b1 opened this Issue Sep 15, 2015 · 3 comments Projects None yet Labels Bug Milestone No milestone Assignees No one assigned 2 participants 0x00b1 commented Sep 15, 2015 From Travis: https://s3.amazonaws.com/archive.travis-ci.org/jobs/80351444/log.txt test_01_01_start_and_stop (cellprofiler.tests.test_analysis.TestAnalysis) ... HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 139763498239744: #000: ../../../src/H5Gdeprec.c line 872 in H5Gget_objinfo(): cannot stat object major: Invalid arguments to routine minor: Unable to initialize object #001: ../../../src/H5Gdeprec.c line 999 in H5G_get_objinfo(): name doesn't exist major: Symbol table minor: Object already exists #002: ../../../src/H5Gtraverse.c line 877 in H5G_traverse(): internal path traversal failed major: Symbol table minor: Object not found #003: ../../../src/H5Gtraverse.c line 703 in H5G_traverse_real(): traversal operator failed major: Symbol table minor: Callback failed #004: ../../../src/H5Gdeprec.c line 903 in H5G_get_objinfo_cb(): name doesn't exist major: Symbol table minor: Object not found HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 139763498239744: #000: ../../../src/H5Gdeprec.c line 872 in H5Gget_objinfo(): cannot stat object major: Invalid arguments to routine minor: Unable to initialize object #001: ../../../src/H5Gdeprec.c line 999 in H5G_get_objinfo(): name doesn't exist major: Symbol table minor: Object already exists #002: ../../../src/H5Gtraverse.c line 877 in H5G_traverse(): internal path traversal failed major: Symbol table minor: Object not found #003: ../../../src/H5Gtraverse.c line 703 in H5G_traverse_real(): traversal operator failed major: Symbol table minor: Callback failed #004: ../../../src/H5Gdeprec.c line 903 in H5G_get_objinfo_cb(): name doesn't exist major: Symbol table minor: Object not found HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 139763498239744: #000: ../../../src/H5Gdeprec.c line 872 in H5Gget_objinfo(): cannot stat object major: Invalid arguments to routine minor: Unable to initialize object #001: ../../../src/H5Gdeprec.c line 999 in H5G_get_objinfo(): name doesn't exist major: Symbol table minor: Object already exists #002: ../../../src/H5Gtraverse.c line 877 in H5G_traverse(): internal path traversal failed
Sedov, Sod, Pancake, ... Next message: [FLASH-USERS] Error detected in HDF5 while running ./flash3 for Sedov, Sod, Pancake, ... Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] I had errors like this before. My problem was that I was not correctly interfacing with HDF5 because of intergace issues. See this webpage for an overview: http://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html My solution was essentially to set this line in my Makefile.h file: CFLAGS_HDF5 = -I $(HDF5_PATH)/include -D H5_USE_16_API Now my version of HDF5 is serial. But I definitely saw errors like you had and they went away with the flag change. Sam On Wed, 31 Mar 2010, huong luu wrote: > Hi, > I am a newbie to Flash and I am trying to https://github.com/CellProfiler/CellProfiler/issues/1565 get FLASH code running (any > simulation problem is good). > I have install MPICH2, HDF5-1.8.4 (with default api version = v1.6 and > enable parallel). I did successfully make the executable file flash3 appear. > However, when I run it, then it has error detected. The weird thing is I > tried with Sedov, Sod, Pancake problem and all of them have similar error > messages. > For more details, here is what I did: > > ./setup Sedov http://flash.uchicago.edu/pipermail/flash-users/2010-March/000667.html -auto > cd object > gmake > cp ../source/Simulation/SimulationMain/Sedov/flash.par ./ > ./flash3 > > ===> >
] [ subject ] [ author ] On Tue, Mar 30, 2010 at 2:18 PM, Elena Pourmal
when I try to run a very simple python program using pyminc: The minimal program that creates the error: #! /usr/bin/python import pyminc.volumes.factory as pyminc inputfilename = "t1.minc2.posdir.mnc" outputfilename = "copy.mnc" infile = pyminc.volumeFromFile(inputfilename) outfile = pyminc.volumeLikeFile(inputfilename, outputfilename) outfile.writeFile() outfile.closeVolume() infile.closeVolume() The error: HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value The error with PYMINCDEBUG set: HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value sizes [192, 256, 192] separations [0.999999999999998, 1.0, 1.0] starts [-103.827645851979, -111.44957556808501, -84.49910974372] dimnames: ['zspace', 'yspace', 'xspace'] sizes [192, 256, 192] separations [0.999999999999998, 1.0, 1.0] starts [-103.827645851979, -111.44957556808501, -84.49910974372] dimnames: ['zspace', 'yspace', 'xspace'] 0 48381856 c_void_p(48388544) z