Error Detected In Hdf5
Contents |
here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the
Hdf5-diag Error Detected In Hdf5 (1.8.6) Thread 0
workings and policies of this site About Us Learn more about hdf5 error codes Stack Overflow the company Business Learn more about hiring developers or posting ads with us Stack Overflow Questions
H5fopen() Unable To Open File
Jobs Documentation Tags Users Badges Ask Question x Dismiss Join the Stack Overflow Community Stack Overflow is a community of 4.7 million programmers, just like you, helping each other. h5eset_auto Join them; it only takes a minute: Sign up HDF5-DIAG: Error detected in HDF5 (1.8.11) up vote 4 down vote favorite I am trying to load hdf5 in caffe, it is not working. I checked the paths and even able to view hdf file using viewer. Everything is ok but caffe cant seem to load. I write the hdf5 caffe hdf5 example using a python script like this, where X and labels are numpy arrays. f = h5py.File("facialkp.hd5", "w") f.create_dataset("data", data=X, compression="gzip", compression_opts=4) f.create_dataset("label", data=labels, compression="gzip", compression_opts=4) Here is the entire problem. root@pbu-OptiPlex-740-Enhanced:/home/pbu/Desktop# ./facialkp_train.sh I0119 19:55:50.779419 9905 caffe.cpp:103] Use CPU. I0119 19:55:51.152626 9905 caffe.cpp:107] Starting Optimization I0119 19:55:51.152817 9905 solver.cpp:32] Initializing solver from parameters: test_iter: 1000 test_interval: 1000 base_lr: 0.01 display: 1000 max_iter: 10000 lr_policy: "step" gamma: 0.1 momentum: 0.9 weight_decay: 0.0005 stepsize: 5000 snapshot: 10000 snapshot_prefix: "/home/pbu/Desktop/tmp" solver_mode: CPU net: "/home/pbu/Desktop/facialkp.prototxt" I0119 19:55:51.152936 9905 solver.cpp:67] Creating training net from net file: /home/pbu/Desktop/facialkp.prototxt I0119 19:55:51.153211 9905 net.cpp:39] Initializing net from parameters: name: "LogReg" layers { top: "data" top: "label" name: "data" type: HDF5_DATA hdf5_data_param { source: "facialkp.hd5" batch_size: 10 } include { phase: TRAIN } } layers { bottom: "data" top: "ip" name: "ip" type: INNER_PRODUCT inner_product_param { num_output: 30 } } layers { bottom: "ip" bottom: "label" top: "loss" name: "loss" type: EUCLIDEAN_LOSS } state { phase: TRAIN } I0119 19:55:51.153457 9905 net.cpp:67] Creating Layer data I0119 19:55:51.153486 9905 net.cpp:356] data -> data I0119 19:55:51.153524
Sign in Pricing Blog Support Search GitHub This repository Watch 1,604 Star 13,013 Fork 7,968 BVLC/caffe Code Issues 553 Pull requests 265 Projects 0 Wiki Pulse Graphs New issue HDF5 crashed when using layer HDF5_OUTPUT #1726 Open tartavull opened this Issue Jan 15, 2015 · 11 comments Projects None yet Labels None yet Milestone No milestone Assignees No one assigned 8 participants tartavull commented http://stackoverflow.com/questions/28031841/hdf5-diag-error-detected-in-hdf5-1-8-11 Jan 15, 2015 it works on the beginning but it crashes when rewriting to it I0114 19:41:35.961170 18670 hdf5_output_layer.cpp:33] Saving HDF5 file/usr/people/me/caffe/examples/test/test_prediction.h5 I0114 19:41:35.962885 18670 hdf5_output_layer.cpp:38] Successfully saved 100 rows I0114 19:41:35.986912 18670 hdf5_output_layer.cpp:33] Saving HDF5 file/usr/people/me/caffe/examples/test/test_prediction.h5 HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 140309532535360: #000: ../../../src/H5D.c line 170 in H5Dcreate2(): unable https://github.com/BVLC/caffe/issues/1726 to create dataset major: Dataset minor: Unable to initialize object #1: ../../../src/H5Dint.c line 439 in H5D__create_named(): unable to create and link to dataset major: Dataset minor: Unable to initialize object #2: ../../../src/H5L.c line 1638 in H5L_link_object(): unable to create new link to object major: Links minor: Unable to initialize object #3: ../../../src/H5L.c line 1882 in H5L_create_real(): can't insert link major: Symbol table minor: Unable to insert object #4: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed major: Symbol table minor: Object not found #5: ../../../src/H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed major: Symbol table minor: Callback failed #6: ../../../src/H5L.c line 1674 in H5L_link_cb(): name already exists major: Symbol table minor: Object already exists F0114 19:41:35.987098 18670 io.cpp:178] Check failed: status >= 0 (-1 vs. 0) Failed to make float dataset data *** Check failure stack trace: *** @ 0x7f9c5635bdaa (unknown) @ 0x7f9c5635bce4 (unknown) @ 0x7f9c5635b6e6 (unknown) @ 0x7f9c5635e687 (unknown) @ 0x4a0a41 caffe::hdf5_save_nd_datas
Sign in Pricing Blog Support Search GitHub This repository Watch 12 Star 107 Fork 63 JuliaIO/HDF5.jl Code Issues 55 Pull requests 7 Projects 0 Pulse Graphs https://github.com/JuliaIO/HDF5.jl/issues/298 New issue import/using HDF fails: HDF5-DIAG: Error detected in HDF5 (1.10.0) #298 Closed anowacki opened this Issue Apr 26, 2016 · 8 comments Projects None yet Labels None yet http://fenicsproject.org/qa/6141/errors-when-loading-hdf5-files Milestone No milestone Assignees No one assigned 5 participants anowacki commented Apr 26, 2016 • edited First of all, apologies that I don't have time to look into this error detected more myself before submitting. Attempting to use HDF with Julia 0.4.5, on OS X 10.10.5, using HDF5 (both installed via MacPorts), gives an error when trying to using or import it. The relevant part of the output is: INFO: Recompiling stale cache file /Users/nowacki/.julia/lib/v0.4/HDF5.ji for module HDF5. INFO: Recompiling stale cache file /Users/nowacki/.julia/lib/v0.4/Blosc.ji for module Blosc. HDF5-DIAG: Error detected in HDF5 (1.10.0) error detected in thread 0: #000: H5P.c line 254 in H5Pcreate(): not a property list class major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.10.0) thread 0: #000: H5Pstrcpl.c line 171 in H5Pset_char_encoding(): can't find object for ID major: Object atom minor: Unable to find atom information (already closed?) #001: H5Pint.c line 3817 in H5P_object_verify(): property list is not a member of the class major: Property lists minor: Unable to register new atom #002: H5Pint.c line 3767 in H5P_isa_class(): not a property list major: Invalid arguments to routine minor: Inappropriate type ERROR: InitError: Error setting char encoding in h5p_set_char_encoding at /Users/nowacki/.julia/v0.4/HDF5/src/plain.jl:1951 in __init__ at /Users/nowacki/.julia/v0.4/HDF5/src/plain.jl:2320 in _require_from_serialized at ./loading.jl:84 in _require_from_serialized at /opt/local/lib/julia/sys.dylib in require at /opt/local/lib/julia/sys.dylib in process_options at /opt/local/lib/julia/sys.dylib in _start at /opt/local/lib/julia/sys.dylib during initialization of module HDF5 See the full log, including versioninfo() from the command: $ rm -rf ~/.julia/v0.4; julia --check-bounds=yes -e "versioninfo(); Pkg.update(); Pkg.add(\"HDF5\"); using HDF5" This does work with 0.5.0-dev+2440, however (despite all the warnings). Please do let me know what I can do to help diagnose the problem, and thanks for the hard wo
load a hdf5/xdmf file using the following dolfin commands from dolfin import * mesh = Mesh('example.xdmf') When I do this I get the following error message HDF5-DIAG: Error detected in HDF5 (1.8.11) MPI-process 0: #000: ../../../src/H5L.c line 824 in H5Lexists(): unable to get link info major: Symbol table minor: Object not found #001: ../../../src/H5L.c line 2765 in H5L_exists(): path doesn't exist major: Symbol table minor: Object already exists #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed major: Symbol table minor: Object not found #003: ../../../src/H5Gtraverse.c line 755 in H5G_traverse_real(): component not found major: Symbol table minor: Object not found HDF5-DIAG: Error detected in HDF5 (1.8.11) MPI-process 0: #000: ../../../src/H5L.c line 824 in H5Lexists(): unable to get link info major: Symbol table minor: Object not found #001: ../../../src/H5L.c line 2765 in H5L_exists(): path doesn't exist major: Symbol table minor: Object already exists #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed major: Symbol table minor: Object not found #003: ../../../src/H5Gtraverse.c line 755 in H5G_traverse_real(): component not found major: Symbol table minor: Object not found HDF5-DIAG: Error detected in HDF5 (1.8.11) MPI-process 0: #000: ../../../src/H5D.c line 334 in H5Dopen2(): not found major: Dataset minor: Object not found #001: ../../../src/H5Gloc.c line 430 in H5G_loc_find(): can't find object major: Symbol table minor: Object not found #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed major: Symbol table minor: Object not found #003: ../../../src/H5Gtraverse.c line 755 in H5G_traverse_real(): component not found major: Symbol table minor: Object not found HDF5-DIAG: Error detected in HDF5 (1.8.11) MPI-process 0: #000: ../../../src/H5D.c line 437 in H5Dget_space(): not a dataset major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.11) MPI-process 0: #000: ../../../src/H5S.c line 794 in H5Sget_simple_extent_ndims(): not a dataspace major: Invalid arguments to routine minor: Inappropriate type Traceback (most recent call last): File "test2.py", line 3, in mesh = Mesh('example.xdmf') File "/home/les/install/fenics/1.4.0/lib/python2.7/site-packages/dolfin/mesh/meshes.py", line 66, in init cpp.Mesh.cppinit(self, *args, **kwargs) File "/home/les/install/fenics/1.4.0/lib/python2.7/site-packages/dolfin/cpp/mesh.py", line 1592, in __init__ _mesh.Mesh_swiginit(self,_mesh.new_Mesh(*args)) Exception: std::bad_alloc When