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h5md / VMD-h5mdplugin

This plugin enables VMD to display data stored in h5 files that are structured according to the H5MD specifications (http://nongnu.org/h5md/)
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Error when compiling under Ubuntu 14.04 #10

Closed jkrajniak closed 9 years ago

jkrajniak commented 9 years ago

I have tried to compile plugin under Ubuntu 14.04, but unfortunately it fails. I had to change the HDF5LDFLAGS to /usr/lib/x86_64-linux-gnu (as there are the libraries) but it does not helps. Below is the compilation log:

$ make gcc -Wall -std=c99 -O0 -pedantic -fPIC -g -shared -Wl,--no-undefined -L/usr/lib/x86_64-linux-gnu -L. -lhdf5_hl -lhdf5 libh5md.o -o libh5md.so libh5md.o: In function discover_all_groups': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:60: undefined reference toH5Lvisit' libh5md.o: In function check_for_pos_dataset': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:71: undefined reference toH5Gget_objinfo' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:74: undefined reference to H5Dopen2' libh5md.o: In functionmodify_information_about_file_content': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:91: undefined reference to H5Dopen2' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:96: undefined reference toH5Dopen2' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:112: undefined reference to H5Dget_type' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:113: undefined reference toH5Tget_class' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:114: undefined reference to H5Tget_order' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:116: undefined reference toH5Tget_size' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:117: undefined reference to H5Dget_space' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:118: undefined reference toH5Sget_simple_extent_ndims' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:120: undefined reference to H5Sget_simple_extent_dims' libh5md.o: In functioncheck_compatibility': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:138: undefined reference to H5Dget_space' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:139: undefined reference toH5Sget_simple_extent_ndims' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:141: undefined reference to H5Sget_simple_extent_dims' libh5md.o: In functionh5md_open': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:159: undefined reference to H5check_version' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:159: undefined reference toH5Fopen' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:161: undefined reference to H5check_version' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:161: undefined reference toH5Fopen' libh5md.o: In function h5md_close': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:180: undefined reference toH5Dclose' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:181: undefined reference to H5Dclose' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:185: undefined reference toH5Fclose' libh5md.o: In function h5md_get_timestep': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:248: undefined reference toH5Dget_space' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:262: undefined reference to H5Sselect_hyperslab' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:271: undefined reference toH5Screate_simple' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:285: undefined reference to H5Sselect_hyperslab' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:292: undefined reference toH5open' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:292: undefined reference to H5T_NATIVE_FLOAT_g' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:293: undefined reference toH5Dread' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:294: undefined reference to H5Sclose' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:295: undefined reference toH5Sclose' libh5md.o: In function h5md_read_timeindependent_dataset_automatically': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:327: undefined reference toH5Dopen2' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:332: undefined reference to H5Dget_type' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:333: undefined reference toH5Tget_class' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:335: undefined reference to H5Tget_size' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:336: undefined reference toH5Dget_space' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:337: undefined reference to H5Sget_simple_extent_ndims' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:339: undefined reference toH5Sget_simple_extent_dims' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:354: undefined reference to H5Dread' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:367: undefined reference toH5Dread' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:380: undefined reference to H5Sget_simple_extent_dims' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:384: undefined reference toH5Tis_variable_str' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:392: undefined reference to H5open' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:392: undefined reference toH5T_C_S1_g' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:392: undefined reference to H5Tcopy' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:393: undefined reference toH5Tset_size' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:394: undefined reference to H5Dread' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:396: undefined reference toH5Tclose' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:400: undefined reference to H5open' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:400: undefined reference toH5T_C_S1_g' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:400: undefined reference to H5Tcopy' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:401: undefined reference toH5Tset_size' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:402: undefined reference to H5Dread' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:404: undefined reference toH5Tclose' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:420: undefined reference to H5Dclose' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:421: undefined reference toH5Sclose' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:422: undefined reference to H5Tclose' libh5md.o: In functionh5md_read_timeindependent_dataset_int': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:455: undefined reference to H5open' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:455: undefined reference toH5T_NATIVE_INT_g' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:455: undefined reference to H5Tget_class' libh5md.o: In functionh5md_get_length_of_one_dimensional_dataset': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:462: undefined reference to H5Dopen2' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:463: undefined reference toH5Dget_space' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:464: undefined reference to H5Sget_simple_extent_ndims' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:466: undefined reference toH5Sget_simple_extent_dims' libh5md.o: In function h5md_hide_hdf5_error_messages': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:479: undefined reference toH5Eset_auto2' libh5md.o: In function h5md_show_hdf5_error_messages': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:483: undefined reference toH5Eprint2' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:483: undefined reference to H5Eset_auto2' libh5md.o: In functionh5md_get_all_species_infromation': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:502: undefined reference to H5Dget_space' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:511: undefined reference toH5Sselect_hyperslab' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:519: undefined reference to H5Screate_simple' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:531: undefined reference toH5Sselect_hyperslab' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:537: undefined reference to H5open' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:537: undefined reference toH5T_NATIVE_INT_g' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:538: undefined reference to H5Dread' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:539: undefined reference toH5Sclose' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:540: undefined reference to H5Sclose' libh5md.o: In functionh5md_create_file': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:560: undefined reference to H5check_version' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:560: undefined reference toH5Fcreate' libh5md.o: In function h5md_write_dataset': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:582: undefined reference toH5open' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:582: undefined reference to H5P_CLS_LINK_CREATE_g' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:582: undefined reference toH5Pcreate' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:583: undefined reference to H5Pset_create_intermediate_group' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:588: undefined reference toH5open' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:588: undefined reference to H5P_CLS_DATASET_CREATE_g' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:588: undefined reference toH5Pcreate' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:589: undefined reference to H5Pset_chunk' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:591: undefined reference toH5Tget_class' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:595: undefined reference to H5Pset_fill_value' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:601: undefined reference toH5Pset_fill_value' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:607: undefined reference to H5Pset_fill_value' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:620: undefined reference toH5Screate_simple' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:622: undefined reference to H5Dcreate2' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:623: undefined reference toH5Dwrite' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:626: undefined reference to H5Dclose' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:627: undefined reference toH5Sclose' libh5md.o: In function h5md_append_dataset': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:641: undefined reference toH5Dopen2' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:644: undefined reference to H5Dget_type' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:645: undefined reference toH5Tget_class' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:646: undefined reference to H5Dget_space' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:647: undefined reference toH5Sget_simple_extent_ndims' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:649: undefined reference to H5Sget_simple_extent_dims' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:652: undefined reference toH5Tget_class' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:664: undefined reference to H5Dextend' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:667: undefined reference toH5Dget_space' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:675: undefined reference to H5Sselect_hyperslab' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:676: undefined reference toH5Screate_simple' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:677: undefined reference to H5Dwrite' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:682: undefined reference toH5Sclose' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:683: undefined reference to H5Sclose' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:687: undefined reference toH5Tclose' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:688: undefined reference to H5Sclose' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:689: undefined reference toH5Dclose' libh5md.o: In function get_fill_value': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:698: undefined reference toH5Dopen2' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:699: undefined reference to H5Dget_create_plist' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:701: undefined reference toH5Dget_type' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:702: undefined reference to H5Tget_class' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:705: undefined reference toH5open' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:705: undefined reference to H5T_NATIVE_INT_g' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:705: undefined reference toH5Pget_fill_value' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:710: undefined reference to H5open' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:710: undefined reference toH5T_NATIVE_FLOAT_g' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:710: undefined reference to H5Pget_fill_value' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:715: undefined reference toH5Pget_fill_value' libh5md.o: In function h5md_delete_dataset': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:734: undefined reference toH5Dopen2' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:736: undefined reference to H5Ldelete' libh5md.o: In functionh5md_set_author': /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:744: undefined reference to H5Gcreate2' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:750: undefined reference toH5LTset_attribute_string' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:752: undefined reference to H5LTset_attribute_string' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:757: undefined reference toH5LTset_attribute_string' /home/jakub/project/software/VMD-h5mdplugin/libh5md.c:759: undefined reference to `H5LTset_attribute_string' collect2: error: ld returned 1 exit status make: *\ [libh5md.so] Error 1

jonaslandsgesell commented 9 years ago

Thanks for the fix. I have merged your commit into the main branch.