Errors Compiling C Program to Create HDF5 File

Gokop · January 13, 2014, 4:09pm

Dear HDF5 Forum Members,
Please I compiled a c code successfully but when running the executable to produce the >h5 file I have the following errors (I attached the c code and input file). The output of the input file are all zeros. See errors below:

ubuntu@ip-10-185-8-233:~/HDF5/myExamples$ /usr/local/hdf5/bin/h5cc -o myh5ex_g_pwa_interface myh5ex_g_pwa_interface.c
ubuntu@ip-10-185-8-233:~/HDF5/myExamples$ ./myh5ex_g_pwa_interface
HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
#000: H5D.c line 170 in H5Dcreate2(): unable to create dataset
major: Dataset
minor: Unable to initialize object
#001: H5Dint.c line 439 in H5D__create_named(): unable to create and link to dataset
major: Dataset
minor: Unable to initialize object
#002: H5L.c line 1638 in H5L_link_object(): unable to create new link to object
major: Links
minor: Unable to initialize object
#003: H5L.c line 1882 in H5L_create_real(): can't insert link
major: Symbol table
minor: Unable to insert object
#004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#005: H5Gtraverse.c line 755 in H5G_traverse_real(): component not found
major: Symbol table
minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
#000: H5Dio.c line 231 in H5Dwrite(): can't prepare for writing data
major: Dataset
minor: Write failed
#001: H5Dio.c line 263 in H5D__pre_write(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
#000: H5Dio.c line 137 in H5Dread(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type

/reactionData/arrheniusData/arrheniusParam[0][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[0][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[0][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[1][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[1][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[1][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[2][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[2][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[2][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[3][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[3][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[3][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[4][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[4][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[4][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[5][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[5][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[5][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[6][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[6][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[6][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[7][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[7][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[7][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[8][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[8][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[8][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[9][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[9][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[9][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[10][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[10][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[10][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[11][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[11][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[11][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[12][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[12][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[12][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[13][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[13][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[13][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[14][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[14][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[14][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[15][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[15][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[15][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[16][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[16][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[16][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[17][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[17][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[17][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[18][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[18][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[18][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[19][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[19][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[19][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[20][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[20][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[20][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[21][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[21][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[21][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[22][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[22][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[22][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[23][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[23][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[23][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[24][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[24][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[24][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[25][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[25][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[25][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[26][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[26][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[26][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[27][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[27][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[27][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[28][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[28][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[28][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[29][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[29][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[29][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[30][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[30][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[30][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[31][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[31][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[31][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[32][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[32][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[32][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[33][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[33][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[33][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[34][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[34][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[34][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[35][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[35][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[35][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[36][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[36][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[36][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[37][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[37][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[37][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[38][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[38][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[38][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[39][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[39][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[39][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[40][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[40][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[40][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[41][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[41][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[41][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[42][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[42][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[42][2]: 0.000000
HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
#000: H5D.c line 391 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
Objects in the file:
/ (Group)
/elementData (Group)
/elementData/elementNames (Dataset)
/elementData/elementPrimeID (Dataset)
/phaseData (Group)
/phaseData/eqState (Dataset)
/phaseData/phase (Dataset)
/primeID (Dataset)
/reactionData (Group)
/reactionData/arrheniusData (Group)
/reactionData/arrheniusData/arrheniusPrimeID (Dataset)
/reactionData/falloffData (Group)
/reactionData/falloffData/falloffNames (Dataset)
/reactionData/falloffData/falloffType (Dataset)
/reactionData/rateCoefLinks (Group)
/reactionData/rateCoefLinks/r00009454 (Dataset)
/reactionData/rateCoefLinks/r00009484 (Dataset)
/reactionData/rateCoefLinks/r00009509 (Dataset)
/reactionData/rateCoefLinks/r00011821 (Dataset)
/reactionData/rateCoefLinks/r00011842 (Dataset)
/reactionData/rateCoefLinks/r00011866 (Dataset)
/reactionData/rateCoefLinks/r00012023 (Dataset)
/reactionData/rateCoefLinks/r00012138 (Dataset)
/reactionData/rateCoefLinks/r00012186 (Dataset)
/reactionData/rateCoefLinks/r00012255 (Dataset)
/reactionData/rateCoefLinks/r00013690 (Dataset)
/reactionData/rateCoefLinks/r00013692 (Dataset)
/reactionData/rateCoefLinks/r00013701 (Dataset)
/reactionData/rateCoefLinks/r00013764 (Dataset)
/reactionData/rateCoefLinks/r00013767 (Dataset)
/reactionData/rateCoefLinks/r00013781 (Dataset)
/reactionData/rateCoefLinks/r00013804 (Dataset)
/reactionData/rateCoefLinks/r00013805 (Dataset)
/reactionData/rateCoefLinks/r00013869 (Dataset)
/reactionData/rateCoefLinks/r00015825 (Dataset)
/reactionData/reactionEquations (Dataset)
/reactionData/reactionPrimeID (Dataset)
/reactionData/reactionRateType (Dataset)
/speciesData (Group)
/speciesData/speciesNames (Dataset)
/speciesData/speciesPrimeID (Dataset)
/speciesData/thermoPolynomials (Group)
/speciesData/thermoPolynomials/thermoPrimeID (Dataset)
/speciesData/thermoPolynomials/thermoType (Dataset)
/title (Dataset)
title[0]: PrIMe H2-Mech 1.0
primeID[0]: m00000004
/elementData/elementNames[0]: Ar
/elementData/elementNames[1]: H
/elementData/elementNames[2]: N
/elementData/elementNames[3]: O
/elementData/elementPrimeID[0]: e00000018
/elementData/elementPrimeID[1]: e00000001
/elementData/elementPrimeID[2]: e00000007
/elementData/elementPrimeID[3]: e00000008
/phaseData/eqState[0]: ideal gas
/phaseData/phase[0]: gas
/reactionData/reactionEquations[0]: O + O <=> O2
/reactionData/reactionEquations[1]: H + O <=> OH
/reactionData/reactionEquations[2]: H2 + O <=> OH + H
/reactionData/reactionEquations[3]: HO2 + O <=> OH + O2
/reactionData/reactionEquations[4]: O + H2O2 <=> OH + HO2
/reactionData/reactionEquations[5]: O2 + H <=> HO2
/reactionData/reactionEquations[6]: O2 + H <=> OH + O
/reactionData/reactionEquations[7]: 2 H <=> H2
/reactionData/reactionEquations[8]: OH + H <=> H2O
/reactionData/reactionEquations[9]: HO2 + H <=> H2O + O
/reactionData/reactionEquations[10]: HO2 + H <=> H2 + O2
/reactionData/reactionEquations[11]: HO2 + H <=> 2 OH
/reactionData/reactionEquations[12]: H2O2 + H <=> H2 + HO2
/reactionData/reactionEquations[13]: H2O2 + H <=> OH + H2O
/reactionData/reactionEquations[14]: H2 + OH <=> H2O + H
/reactionData/reactionEquations[15]: 2 OH <=> H2O2
/reactionData/reactionEquations[16]: 2 OH <=> H2O + O
/reactionData/reactionEquations[17]: HO2 + OH <=> H2O + O2
/reactionData/reactionEquations[18]: OH + H2O2 <=> HO2 + H2O
/reactionData/reactionEquations[19]: 2 HO2 <=> H2O2 + O2
/reactionData/reactionPrimeID[0]: r00013869
/reactionData/reactionPrimeID[1]: r00012023
/reactionData/reactionPrimeID[2]: r00012186
/reactionData/reactionPrimeID[3]: r00012138
/reactionData/reactionPrimeID[4]: r00015825
/reactionData/reactionPrimeID[5]: r00011821
/reactionData/reactionPrimeID[6]: r00012255
/reactionData/reactionPrimeID[7]: r00009454
/reactionData/reactionPrimeID[8]: r00013764
/reactionData/reactionPrimeID[9]: r00013804
/reactionData/reactionPrimeID[10]: r00009509
/reactionData/reactionPrimeID[11]: r00011866
/reactionData/reactionPrimeID[12]: r00009484
/reactionData/reactionPrimeID[13]: r00013701
/reactionData/reactionPrimeID[14]: r00013781
/reactionData/reactionPrimeID[15]: r00013690
/reactionData/reactionPrimeID[16]: r00013805
/reactionData/reactionPrimeID[17]: r00013767
/reactionData/reactionPrimeID[18]: r00011842
/reactionData/reactionPrimeID[19]: r00013692
/reactionData/reactionRateType[0]: third body
/reactionData/reactionRateType[1]: third body
/reactionData/reactionRateType[2]: mass action
/reactionData/reactionRateType[3]: mass action
/reactionData/reactionRateType[4]: mass action
/reactionData/reactionRateType[5]: third body
/reactionData/reactionRateType[6]: mass action
/reactionData/reactionRateType[7]: third body
/reactionData/reactionRateType[8]: third body
/reactionData/reactionRateType[9]: mass action
/reactionData/reactionRateType[10]: mass action
/reactionData/reactionRateType[11]: mass action
/reactionData/reactionRateType[12]: mass action
/reactionData/reactionRateType[13]: mass action
/reactionData/reactionRateType[14]: mass action
/reactionData/reactionRateType[15]: unimolecular
/reactionData/reactionRateType[16]: mass action
/reactionData/reactionRateType[17]: sum
/reactionData/reactionRateType[18]: sum
/reactionData/reactionRateType[19]: sum
/reactionData/arrheniusData/arrheniusPrimeID[0]: rk00000016
/reactionData/arrheniusData/arrheniusPrimeID[1]: rk00000017
/reactionData/arrheniusData/arrheniusPrimeID[2]: rk00000022
/reactionData/arrheniusData/arrheniusPrimeID[3]: rk00000015
/reactionData/arrheniusData/arrheniusPrimeID[4]: rk00000003
/reactionData/arrheniusData/arrheniusPrimeID[5]: rk00000004
/reactionData/arrheniusData/arrheniusPrimeID[6]: rk00000009
/reactionData/arrheniusData/arrheniusPrimeID[7]: rk00000002
/reactionData/arrheniusData/arrheniusPrimeID[8]: rk00000005
/reactionData/arrheniusData/arrheniusPrimeID[9]: rk00000002
/reactionData/arrheniusData/arrheniusPrimeID[10]: rk00000003
/reactionData/arrheniusData/arrheniusPrimeID[11]: rk00000006
/reactionData/arrheniusData/arrheniusPrimeID[12]: rk00000007
/reactionData/arrheniusData/arrheniusPrimeID[13]: rk00000009
/reactionData/arrheniusData/arrheniusPrimeID[14]: rk00000011
/reactionData/arrheniusData/arrheniusPrimeID[15]: rk00000015
/reactionData/arrheniusData/arrheniusPrimeID[16]: rk00000042
/reactionData/arrheniusData/arrheniusPrimeID[17]: rk00000019
/reactionData/arrheniusData/arrheniusPrimeID[18]: rk00000020
/reactionData/arrheniusData/arrheniusPrimeID[19]: rk00000023
/reactionData/arrheniusData/arrheniusPrimeID[20]: rk00000024
/reactionData/arrheniusData/arrheniusPrimeID[21]: rk00000010
/reactionData/arrheniusData/arrheniusPrimeID[22]: rk00000011
/reactionData/arrheniusData/arrheniusPrimeID[23]: rk00000014
/reactionData/arrheniusData/arrheniusPrimeID[24]: rk00000009
/reactionData/arrheniusData/arrheniusPrimeID[25]: rk00000002
/reactionData/arrheniusData/arrheniusPrimeID[26]: rk00000007
/reactionData/arrheniusData/arrheniusPrimeID[27]: rk00000020
/reactionData/arrheniusData/arrheniusPrimeID[28]: rk00000008
/reactionData/arrheniusData/arrheniusPrimeID[29]: rk00000020
/reactionData/arrheniusData/arrheniusPrimeID[30]: rk00000015
/reactionData/arrheniusData/arrheniusPrimeID[31]: rk00000030
/reactionData/arrheniusData/arrheniusPrimeID[32]: rk00000023
/reactionData/arrheniusData/arrheniusPrimeID[33]: rk00000024
/reactionData/arrheniusData/arrheniusPrimeID[34]: rk00000029
/reactionData/arrheniusData/arrheniusPrimeID[35]: rk00000022
/reactionData/arrheniusData/arrheniusPrimeID[36]: rk00000012
/reactionData/arrheniusData/arrheniusPrimeID[37]: rk00000002
/reactionData/arrheniusData/arrheniusPrimeID[38]: rk00000003
/reactionData/arrheniusData/arrheniusPrimeID[39]: rk00000003
/reactionData/arrheniusData/arrheniusPrimeID[40]: rk00000004
/reactionData/arrheniusData/arrheniusPrimeID[41]: rk00000002
/reactionData/arrheniusData/arrheniusPrimeID[42]: rk00000003
/reactionData/falloffData/falloffType[0]: troe
/reactionData/falloffData/falloffNames[0]: a
/reactionData/falloffData/falloffNames[1]: T***
/reactionData/falloffData/falloffNames[2]: T*
/reactionData/falloffData/falloffNames[3]: T**
/reactionData/rateCoefLinks/r00009454[0]: rk00000028
/reactionData/rateCoefLinks/r00009484[0]: rk00000008
/reactionData/rateCoefLinks/r00009509[0]: rk00000007
/reactionData/rateCoefLinks/r00011821[0]: rk00000025
/reactionData/rateCoefLinks/r00011842[0]: rk00000043
/reactionData/rateCoefLinks/r00011866[0]: rk00000020
/reactionData/rateCoefLinks/r00012023[0]: rk00000011
/reactionData/rateCoefLinks/r00012138[0]: rk00000002
/reactionData/rateCoefLinks/r00012186[0]: rk00000005
/reactionData/rateCoefLinks/r00012255[0]: rk00000042
/reactionData/rateCoefLinks/r00013690[0]: rk00000042
/reactionData/rateCoefLinks/r00013692[0]: rk00000048
/reactionData/rateCoefLinks/r00013701[0]: rk00000020
/reactionData/rateCoefLinks/r00013764[0]: rk00000017
/reactionData/rateCoefLinks/r00013767[0]: rk00000050
/reactionData/rateCoefLinks/r00013781[0]: rk00000015
/reactionData/rateCoefLinks/r00013804[0]: rk00000002
/reactionData/rateCoefLinks/r00013805[0]: rk00000012
/reactionData/rateCoefLinks/r00013869[0]: rk00000026
/reactionData/rateCoefLinks/r00015825[0]: rk00000003
/speciesData/speciesNames[0]: Ar
/speciesData/speciesNames[1]: N2
/speciesData/speciesNames[2]: H
/speciesData/speciesNames[3]: H2
/speciesData/speciesNames[4]: O
/speciesData/speciesNames[5]: O2
/speciesData/speciesNames[6]: OH
/speciesData/speciesNames[7]: H2O
/speciesData/speciesNames[8]: HO2
/speciesData/speciesNames[9]: H2O2
/speciesData/speciesPrimeID[0]: s00000049
/speciesData/speciesPrimeID[1]: s00010231
/speciesData/speciesPrimeID[2]: s00009800
/speciesData/speciesPrimeID[3]: s00009809
/speciesData/speciesPrimeID[4]: s00010285
/speciesData/speciesPrimeID[5]: s00010295
/speciesData/speciesPrimeID[6]: s00010102
/speciesData/speciesPrimeID[7]: s00009881
/speciesData/speciesPrimeID[8]: s00010103
/speciesData/speciesPrimeID[9]: s00009882
/speciesData/thermoPolynomials/thermoPrimeID[0]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[1]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[2]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[3]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[4]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[5]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[6]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[7]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[8]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[9]: thp00000001
/speciesData/thermoPolynomials/thermoType[0]: NASA7
ubuntu@ip-10-185-8-233:~/HDF5/myExamples$ vim myh5ex_g_pwa_interface.c

Please find my c code and input file attached. Any help is appreciated.

Kind regards
Gokop

myh5ex_g_pwa_interface.c (76.7 KB)

CKSoln_Summary_Plot.csv (205 KB)

Mohamad_Chaarawi · January 13, 2014, 4:32pm

You are creating Dataset37 (/reactionData/arrheniusData/arrheniusParam) on line 427, without creating the intermediate groups (/reactionData AND /reactionData/arrheniusData).
If you want HDF5 to create intermediate groups for you, you have to manually set this with the link creation property list passed to H5Dcreate() using H5Pset_create_intermediate_group().

Thanks,
Mohamad

···

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Gokop Goteng
Sent: Monday, January 13, 2014 10:09 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Errors Compiling C Program to Create HDF5 File

Dear HDF5 Forum Members,
Please I compiled a c code successfully but when running the executable to produce the >h5 file I have the following errors (I attached the c code and input file). The output of the input file are all zeros. See errors below:

ubuntu@ip-10-185-8-233:~/HDF5/myExamples$ /usr/local/hdf5/bin/h5cc -o myh5ex_g_pwa_interface myh5ex_g_pwa_interface.c
ubuntu@ip-10-185-8-233:~/HDF5/myExamples$ ./myh5ex_g_pwa_interface
HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
  #000: H5D.c line 170 in H5Dcreate2(): unable to create dataset
    major: Dataset
    minor: Unable to initialize object
  #001: H5Dint.c line 439 in H5D__create_named(): unable to create and link to dataset
    major: Dataset
    minor: Unable to initialize object
  #002: H5L.c line 1638 in H5L_link_object(): unable to create new link to object
    major: Links
    minor: Unable to initialize object
  #003: H5L.c line 1882 in H5L_create_real(): can't insert link
    major: Symbol table
    minor: Unable to insert object
  #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
    major: Symbol table
    minor: Object not found
  #005: H5Gtraverse.c line 755 in H5G_traverse_real(): component not found
    major: Symbol table
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
  #000: H5Dio.c line 231 in H5Dwrite(): can't prepare for writing data
    major: Dataset
    minor: Write failed
  #001: H5Dio.c line 263 in H5D__pre_write(): not a dataset
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
  #000: H5Dio.c line 137 in H5Dread(): not a dataset
    major: Invalid arguments to routine
    minor: Inappropriate type

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/reactionData/arrheniusData/arrheniusParam[38][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[38][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[38][2]: 0.000000
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/reactionData/arrheniusData/arrheniusParam[40][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[40][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[40][2]: 0.000000
/reactionData/arrheniusData/arrheniusParam[41][0]: 0.000000 /reactionData/arrheniusData/arrheniusParam[41][1]: 0.000000 /reactionData/arrheniusData/arrheniusParam[41][2]: 0.000000
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HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
  #000: H5D.c line 391 in H5Dclose(): not a dataset
    major: Invalid arguments to routine
    minor: Inappropriate type
Objects in the file:
/ (Group)
/elementData (Group)
/elementData/elementNames (Dataset)
/elementData/elementPrimeID (Dataset)
/phaseData (Group)
/phaseData/eqState (Dataset)
/phaseData/phase (Dataset)
/primeID (Dataset)
/reactionData (Group)
/reactionData/arrheniusData (Group)
/reactionData/arrheniusData/arrheniusPrimeID (Dataset)
/reactionData/falloffData (Group)
/reactionData/falloffData/falloffNames (Dataset)
/reactionData/falloffData/falloffType (Dataset)
/reactionData/rateCoefLinks (Group)
/reactionData/rateCoefLinks/r00009454 (Dataset)
/reactionData/rateCoefLinks/r00009484 (Dataset)
/reactionData/rateCoefLinks/r00009509 (Dataset)
/reactionData/rateCoefLinks/r00011821 (Dataset)
/reactionData/rateCoefLinks/r00011842 (Dataset)
/reactionData/rateCoefLinks/r00011866 (Dataset)
/reactionData/rateCoefLinks/r00012023 (Dataset)
/reactionData/rateCoefLinks/r00012138 (Dataset)
/reactionData/rateCoefLinks/r00012186 (Dataset)
/reactionData/rateCoefLinks/r00012255 (Dataset)
/reactionData/rateCoefLinks/r00013690 (Dataset)
/reactionData/rateCoefLinks/r00013692 (Dataset)
/reactionData/rateCoefLinks/r00013701 (Dataset)
/reactionData/rateCoefLinks/r00013764 (Dataset)
/reactionData/rateCoefLinks/r00013767 (Dataset)
/reactionData/rateCoefLinks/r00013781 (Dataset)
/reactionData/rateCoefLinks/r00013804 (Dataset)
/reactionData/rateCoefLinks/r00013805 (Dataset)
/reactionData/rateCoefLinks/r00013869 (Dataset)
/reactionData/rateCoefLinks/r00015825 (Dataset)
/reactionData/reactionEquations (Dataset)
/reactionData/reactionPrimeID (Dataset)
/reactionData/reactionRateType (Dataset)
/speciesData (Group)
/speciesData/speciesNames (Dataset)
/speciesData/speciesPrimeID (Dataset)
/speciesData/thermoPolynomials (Group)
/speciesData/thermoPolynomials/thermoPrimeID (Dataset)
/speciesData/thermoPolynomials/thermoType (Dataset)
/title (Dataset)
title[0]: PrIMe H2-Mech 1.0
primeID[0]: m00000004
/elementData/elementNames[0]: Ar
/elementData/elementNames[1]: H
/elementData/elementNames[2]: N
/elementData/elementNames[3]: O
/elementData/elementPrimeID[0]: e00000018
/elementData/elementPrimeID[1]: e00000001
/elementData/elementPrimeID[2]: e00000007
/elementData/elementPrimeID[3]: e00000008
/phaseData/eqState[0]: ideal gas
/phaseData/phase[0]: gas
/reactionData/reactionEquations[0]: O + O <=> O2
/reactionData/reactionEquations[1]: H + O <=> OH
/reactionData/reactionEquations[2]: H2 + O <=> OH + H
/reactionData/reactionEquations[3]: HO2 + O <=> OH + O2
/reactionData/reactionEquations[4]: O + H2O2 <=> OH + HO2
/reactionData/reactionEquations[5]: O2 + H <=> HO2
/reactionData/reactionEquations[6]: O2 + H <=> OH + O
/reactionData/reactionEquations[7]: 2 H <=> H2
/reactionData/reactionEquations[8]: OH + H <=> H2O
/reactionData/reactionEquations[9]: HO2 + H <=> H2O + O
/reactionData/reactionEquations[10]: HO2 + H <=> H2 + O2
/reactionData/reactionEquations[11]: HO2 + H <=> 2 OH
/reactionData/reactionEquations[12]: H2O2 + H <=> H2 + HO2
/reactionData/reactionEquations[13]: H2O2 + H <=> OH + H2O
/reactionData/reactionEquations[14]: H2 + OH <=> H2O + H
/reactionData/reactionEquations[15]: 2 OH <=> H2O2
/reactionData/reactionEquations[16]: 2 OH <=> H2O + O
/reactionData/reactionEquations[17]: HO2 + OH <=> H2O + O2
/reactionData/reactionEquations[18]: OH + H2O2 <=> HO2 + H2O
/reactionData/reactionEquations[19]: 2 HO2 <=> H2O2 + O2
/reactionData/reactionPrimeID[0]: r00013869
/reactionData/reactionPrimeID[1]: r00012023
/reactionData/reactionPrimeID[2]: r00012186
/reactionData/reactionPrimeID[3]: r00012138
/reactionData/reactionPrimeID[4]: r00015825
/reactionData/reactionPrimeID[5]: r00011821
/reactionData/reactionPrimeID[6]: r00012255
/reactionData/reactionPrimeID[7]: r00009454
/reactionData/reactionPrimeID[8]: r00013764
/reactionData/reactionPrimeID[9]: r00013804
/reactionData/reactionPrimeID[10]: r00009509
/reactionData/reactionPrimeID[11]: r00011866
/reactionData/reactionPrimeID[12]: r00009484
/reactionData/reactionPrimeID[13]: r00013701
/reactionData/reactionPrimeID[14]: r00013781
/reactionData/reactionPrimeID[15]: r00013690
/reactionData/reactionPrimeID[16]: r00013805
/reactionData/reactionPrimeID[17]: r00013767
/reactionData/reactionPrimeID[18]: r00011842
/reactionData/reactionPrimeID[19]: r00013692
/reactionData/reactionRateType[0]: third body
/reactionData/reactionRateType[1]: third body
/reactionData/reactionRateType[2]: mass action
/reactionData/reactionRateType[3]: mass action
/reactionData/reactionRateType[4]: mass action
/reactionData/reactionRateType[5]: third body
/reactionData/reactionRateType[6]: mass action
/reactionData/reactionRateType[7]: third body
/reactionData/reactionRateType[8]: third body
/reactionData/reactionRateType[9]: mass action
/reactionData/reactionRateType[10]: mass action
/reactionData/reactionRateType[11]: mass action
/reactionData/reactionRateType[12]: mass action
/reactionData/reactionRateType[13]: mass action
/reactionData/reactionRateType[14]: mass action
/reactionData/reactionRateType[15]: unimolecular
/reactionData/reactionRateType[16]: mass action
/reactionData/reactionRateType[17]: sum
/reactionData/reactionRateType[18]: sum
/reactionData/reactionRateType[19]: sum
/reactionData/arrheniusData/arrheniusPrimeID[0]: rk00000016
/reactionData/arrheniusData/arrheniusPrimeID[1]: rk00000017
/reactionData/arrheniusData/arrheniusPrimeID[2]: rk00000022
/reactionData/arrheniusData/arrheniusPrimeID[3]: rk00000015
/reactionData/arrheniusData/arrheniusPrimeID[4]: rk00000003
/reactionData/arrheniusData/arrheniusPrimeID[5]: rk00000004
/reactionData/arrheniusData/arrheniusPrimeID[6]: rk00000009
/reactionData/arrheniusData/arrheniusPrimeID[7]: rk00000002
/reactionData/arrheniusData/arrheniusPrimeID[8]: rk00000005
/reactionData/arrheniusData/arrheniusPrimeID[9]: rk00000002
/reactionData/arrheniusData/arrheniusPrimeID[10]: rk00000003
/reactionData/arrheniusData/arrheniusPrimeID[11]: rk00000006
/reactionData/arrheniusData/arrheniusPrimeID[12]: rk00000007
/reactionData/arrheniusData/arrheniusPrimeID[13]: rk00000009
/reactionData/arrheniusData/arrheniusPrimeID[14]: rk00000011
/reactionData/arrheniusData/arrheniusPrimeID[15]: rk00000015
/reactionData/arrheniusData/arrheniusPrimeID[16]: rk00000042
/reactionData/arrheniusData/arrheniusPrimeID[17]: rk00000019
/reactionData/arrheniusData/arrheniusPrimeID[18]: rk00000020
/reactionData/arrheniusData/arrheniusPrimeID[19]: rk00000023
/reactionData/arrheniusData/arrheniusPrimeID[20]: rk00000024
/reactionData/arrheniusData/arrheniusPrimeID[21]: rk00000010
/reactionData/arrheniusData/arrheniusPrimeID[22]: rk00000011
/reactionData/arrheniusData/arrheniusPrimeID[23]: rk00000014
/reactionData/arrheniusData/arrheniusPrimeID[24]: rk00000009
/reactionData/arrheniusData/arrheniusPrimeID[25]: rk00000002
/reactionData/arrheniusData/arrheniusPrimeID[26]: rk00000007
/reactionData/arrheniusData/arrheniusPrimeID[27]: rk00000020
/reactionData/arrheniusData/arrheniusPrimeID[28]: rk00000008
/reactionData/arrheniusData/arrheniusPrimeID[29]: rk00000020
/reactionData/arrheniusData/arrheniusPrimeID[30]: rk00000015
/reactionData/arrheniusData/arrheniusPrimeID[31]: rk00000030
/reactionData/arrheniusData/arrheniusPrimeID[32]: rk00000023
/reactionData/arrheniusData/arrheniusPrimeID[33]: rk00000024
/reactionData/arrheniusData/arrheniusPrimeID[34]: rk00000029
/reactionData/arrheniusData/arrheniusPrimeID[35]: rk00000022
/reactionData/arrheniusData/arrheniusPrimeID[36]: rk00000012
/reactionData/arrheniusData/arrheniusPrimeID[37]: rk00000002
/reactionData/arrheniusData/arrheniusPrimeID[38]: rk00000003
/reactionData/arrheniusData/arrheniusPrimeID[39]: rk00000003
/reactionData/arrheniusData/arrheniusPrimeID[40]: rk00000004
/reactionData/arrheniusData/arrheniusPrimeID[41]: rk00000002
/reactionData/arrheniusData/arrheniusPrimeID[42]: rk00000003
/reactionData/falloffData/falloffType[0]: troe
/reactionData/falloffData/falloffNames[0]: a
/reactionData/falloffData/falloffNames[1]: T***
/reactionData/falloffData/falloffNames[2]: T*
/reactionData/falloffData/falloffNames[3]: T**
/reactionData/rateCoefLinks/r00009454[0]: rk00000028
/reactionData/rateCoefLinks/r00009484[0]: rk00000008
/reactionData/rateCoefLinks/r00009509[0]: rk00000007
/reactionData/rateCoefLinks/r00011821[0]: rk00000025
/reactionData/rateCoefLinks/r00011842[0]: rk00000043
/reactionData/rateCoefLinks/r00011866[0]: rk00000020
/reactionData/rateCoefLinks/r00012023[0]: rk00000011
/reactionData/rateCoefLinks/r00012138[0]: rk00000002
/reactionData/rateCoefLinks/r00012186[0]: rk00000005
/reactionData/rateCoefLinks/r00012255[0]: rk00000042
/reactionData/rateCoefLinks/r00013690[0]: rk00000042
/reactionData/rateCoefLinks/r00013692[0]: rk00000048
/reactionData/rateCoefLinks/r00013701[0]: rk00000020
/reactionData/rateCoefLinks/r00013764[0]: rk00000017
/reactionData/rateCoefLinks/r00013767[0]: rk00000050
/reactionData/rateCoefLinks/r00013781[0]: rk00000015
/reactionData/rateCoefLinks/r00013804[0]: rk00000002
/reactionData/rateCoefLinks/r00013805[0]: rk00000012
/reactionData/rateCoefLinks/r00013869[0]: rk00000026
/reactionData/rateCoefLinks/r00015825[0]: rk00000003
/speciesData/speciesNames[0]: Ar
/speciesData/speciesNames[1]: N2
/speciesData/speciesNames[2]: H
/speciesData/speciesNames[3]: H2
/speciesData/speciesNames[4]: O
/speciesData/speciesNames[5]: O2
/speciesData/speciesNames[6]: OH
/speciesData/speciesNames[7]: H2O
/speciesData/speciesNames[8]: HO2
/speciesData/speciesNames[9]: H2O2
/speciesData/speciesPrimeID[0]: s00000049
/speciesData/speciesPrimeID[1]: s00010231
/speciesData/speciesPrimeID[2]: s00009800
/speciesData/speciesPrimeID[3]: s00009809
/speciesData/speciesPrimeID[4]: s00010285
/speciesData/speciesPrimeID[5]: s00010295
/speciesData/speciesPrimeID[6]: s00010102
/speciesData/speciesPrimeID[7]: s00009881
/speciesData/speciesPrimeID[8]: s00010103
/speciesData/speciesPrimeID[9]: s00009882
/speciesData/thermoPolynomials/thermoPrimeID[0]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[1]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[2]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[3]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[4]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[5]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[6]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[7]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[8]: thp00000001
/speciesData/thermoPolynomials/thermoPrimeID[9]: thp00000001
/speciesData/thermoPolynomials/thermoType[0]: NASA7
ubuntu@ip-10-185-8-233:~/HDF5/myExamples$ vim myh5ex_g_pwa_interface.c

Please find my c code and input file attached. Any help is appreciated.
Kind regards
Gokop