Thank you again. I have just tried the issue with Ubuntu 12.04 x86_64 Server and, SURPRISINGLY, just like Debian and Fedora, it did not have any issues. The only impacted OS seems to be the Ubuntu 12.04 x86._64 Desktop version. This seems to be an issue/bug related to the OS rather than HDF5 itself.
Regards, Ekin Akoglu On 31 October 2013 23:42, Elena Pourmal <[email protected]> wrote: > > > > > On Oct 31, 2013, at 4:58 PM, Ekin Akoglu <[email protected]> wrote: > > Thank you, Elena. It works with the modification you have suggested. > However, one thing remains unclear to me. According to my HDF5 > configuration, I have both shared and static library support. But this > issue only occured in Ubuntu 12.04 x86_64 but not on Debian 7 x86_64 or > Fedora 19 x86_64. Is this a bug of HDF5 package or the OS? > > This I don't know :-) > > Allen just told me that Ubuntu is the only system that has static dl > library. We will need to investigate. > > Elena > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Elena Pourmal The HDF Group http://hdfgroup.org > 1800 So. Oak St., Suite 203, Champaign IL 61820 > 217.531.6112 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Regards, > > Ekin Akoglu > > On 31 October 2013 22:48, Elena Pourmal <[email protected]> wrote: > >> Hi Ekin, >> >> "-show" is misleading (I will need to discuss it with the developers and >> see how we can enhance it). I reproduced the problem on CentOS5. >> >> If you run "h5fc -echo h5ex_t_arrayatt_F03.f90" you will see that there >> are two steps: >> >> 1. Compile to create an object file >> 2. Link the object file to create executable >> >> Try the modified command like this (name of the source file should be >> BEFORE linking flags) >> >> $ gfortran -m64 -I/usr/local/hdf5-1.8.11/include *h5ex_t_arrayatt_F03.f90 >> * -L/usr/local/hdf5-1.8.11/lib >> /usr/local/hdf5-1.8.11/lib/libhdf5hl_fortran.a >> /usr/local/hdf5-1.8.11/lib/libhdf5_hl.a >> /usr/local/hdf5-1.8.11/lib/libhdf5_fortran.a >> /usr/local/hdf5-1.8.11/lib/libhdf5.a -lz -lrt -ldl -lm -Wl,-rpath >> -Wl,/usr/local/hdf5-1.8.11/lib >> >> Elena >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Elena Pourmal The HDF Group http://hdfgroup.org >> 1800 So. Oak St., Suite 203, Champaign IL 61820 >> 217.531.6112 >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> >> >> >> On Oct 31, 2013, at 10:31 AM, Ekin Akoglu <[email protected]> wrote: >> >> Dear all, >> >> Further, I would like to supplement my previous mail with my HDF5 >> configuration. So as you will see below, both shared and static libraries >> are already enabled: >> >> SUMMARY OF THE HDF5 CONFIGURATION >> ================================= >> >> General Information: >> ------------------- >> HDF5 Version: 1.8.11 >> Configured on: Thu Oct 31 12:03:54 CET 2013 >> Configured by: eakoglu@nb-ekin >> Configure mode: production >> Host system: x86_64-unknown-linux-gnu >> Uname information: Linux nb-ekin 3.8.0-32-generic >> #47~precise1-Ubuntu SMP Wed Oct 2 16:19:35 UTC 2013 x86_64 x86_64 x86_64 >> GNU/Linux >> Byte sex: little-endian >> Libraries: static, shared >> Installation point: /usr/local/hdf5-1.8.11 >> >> Compiling Options: >> ------------------ >> Compilation Mode: production >> C Compiler: /usr/bin//gcc >> CFLAGS: -O0 >> H5_CFLAGS: -std=c99 -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 -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 >> -Wstrict-aliasing -Wstrict-overflow=5 -Wjump-misses-init >> -Wunsuffixed-float-constants -Wdouble-promotion -Wsuggest-attribute=const >> -Wtrampolines -O3 -fomit-frame-pointer -finline-functions >> AM_CFLAGS: >> CPPFLAGS: >> H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L -DNDEBUG >> -UH5_DEBUG_API >> AM_CPPFLAGS: -D_LARGEFILE_SOURCE >> -D_LARGEFILE64_SOURCE -D_BSD_SOURCE >> Shared C Library: yes >> Static C Library: yes >> Statically Linked Executables: no >> LDFLAGS: >> H5_LDFLAGS: >> AM_LDFLAGS: >> Extra libraries: -lz -lrt -ldl -lm >> Archiver: ar >> Ranlib: ranlib >> Debugged Packages: >> API Tracing: no >> >> Languages: >> ---------- >> Fortran: yes >> Fortran Compiler: /usr/bin//gfortran >> Fortran 2003 Compiler: yes >> Fortran Flags: -m64 >> H5 Fortran Flags: >> AM Fortran Flags: >> Shared Fortran Library: yes >> Static Fortran Library: yes >> >> 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 >> >> >> >> >> >> Regards, >> >> Ekin Akoglu >> >> On 31 October 2013 16:04, Ekin Akoglu <[email protected]> wrote: >> >>> Dear all, >>> >>> Following the issue raised and considering Elena's suggestion on this >>> issue, I tried an experiment on an Ubuntu 12.04 x64 system. The "h5fc >>> -show" output is like this on the system: >>> >>> gfortran -m64 -I/usr/local/hdf5-1.8.11/include >>> -L/usr/local/hdf5-1.8.11/lib /usr/local/hdf5-1.8.11/lib/libhdf5hl_fortran.a >>> /usr/local/hdf5-1.8.11/lib/libhdf5_hl.a >>> /usr/local/hdf5-1.8.11/lib/libhdf5_fortran.a >>> /usr/local/hdf5-1.8.11/lib/libhdf5.a -lz -lrt -ldl -lm -Wl,-rpath >>> -Wl,/usr/local/hdf5-1.8.11/lib >>> >>> Using h5fc to compile the h5ex_t_arrayatt_F03.f90 example file from HDF5 >>> website as: >>> >>> $ h5fc h5ex_t_arrayatt_F03.f90 >>> >>> was successful. However, replacing h5fc with its whole output above like: >>> >>> $ gfortran -m64 -I/usr/local/hdf5-1.8.11/include >>> -L/usr/local/hdf5-1.8.11/lib /usr/local/hdf5-1.8.11/lib/libhdf5hl_fortran.a >>> /usr/local/hdf5-1.8.11/lib/libhdf5_hl.a >>> /usr/local/hdf5-1.8.11/lib/libhdf5_fortran.a >>> /usr/local/hdf5-1.8.11/lib/libhdf5.a -lz -lrt -ldl -lm -Wl,-rpath >>> -Wl,/usr/local/hdf5-1.8.11/lib h5ex_t_arrayatt_F03.f90 >>> >>> to compile the same example file fails with the output below: >>> >>> /tmp/ccAADKQ7.o: In function `MAIN__': >>> h5ex_t_arrayatt_F03.f90:(.text+0x1f): undefined reference to >>> `__h5lib_MOD_h5open_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x11e): undefined reference to >>> `__h5f_MOD_h5fcreate_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x151): undefined reference to >>> `__h5t_MOD_h5tarray_create_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x173): undefined reference to >>> `__h5t_MOD_h5tarray_create_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x18b): undefined reference to >>> `__h5s_MOD_h5screate_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x1db): undefined reference to >>> `__h5d_MOD_h5dcreate_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x1f1): undefined reference to >>> `__h5s_MOD_h5sclose_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x217): undefined reference to >>> `__h5s_MOD_h5screate_simple_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x25a): undefined reference to >>> `__h5a_MOD_h5acreate_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x27d): undefined reference to >>> `__h5a_provisional_MOD_h5awrite_ptr' >>> h5ex_t_arrayatt_F03.f90:(.text+0x290): undefined reference to >>> `__h5a_MOD_h5aclose_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x2a3): undefined reference to >>> `__h5d_MOD_h5dclose_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x2b9): undefined reference to >>> `__h5s_MOD_h5sclose_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x2cc): undefined reference to >>> `__h5t_MOD_h5tclose_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x2df): undefined reference to >>> `__h5t_MOD_h5tclose_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x2f2): undefined reference to >>> `__h5f_MOD_h5fclose_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x31b): undefined reference to >>> `__h5f_MOD_h5fopen_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x340): undefined reference to >>> `__h5d_MOD_h5dopen_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x365): undefined reference to >>> `__h5a_MOD_h5aopen_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x37c): undefined reference to >>> `__h5a_MOD_h5aget_type_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x391): undefined reference to >>> `__h5t_MOD_h5tget_array_dims_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x3ab): undefined reference to >>> `__h5a_MOD_h5aget_space_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x3c7): undefined reference to >>> `__h5s_MOD_h5sget_simple_extent_dims_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x642): undefined reference to >>> `__h5t_MOD_h5tarray_create_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x665): undefined reference to >>> `__h5a_provisional_MOD_h5aread_ptr' >>> h5ex_t_arrayatt_F03.f90:(.text+0x9be): undefined reference to >>> `__h5a_MOD_h5aclose_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x9d1): undefined reference to >>> `__h5d_MOD_h5dclose_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x9e7): undefined reference to >>> `__h5s_MOD_h5sclose_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0x9fa): undefined reference to >>> `__h5t_MOD_h5tclose_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0xa0d): undefined reference to >>> `__h5t_MOD_h5tclose_f' >>> h5ex_t_arrayatt_F03.f90:(.text+0xa20): undefined reference to >>> `__h5f_MOD_h5fclose_f' >>> collect2: ld returned 1 exit status >>> >>> >>> How come could this be possible? It does not make any sense to me. I >>> would be glad if you share your thoughts on the issue. >>> >>> Best regards, >>> >>> Ekin Akoglu >>> >>> On 20 June 2013 16:47, Elena Pourmal <[email protected]> wrote: >>> >>>> Please check that you use -ldl when you link your application (or use >>>> h5cc!) >>>> >>>> We introduced dynamical loading of the HDF5 filters in HDF5 1.8.11 and >>>> this library is required now. >>>> >>>> Elena >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> Elena Pourmal The HDF Group http://hdfgroup.org >>>> 1800 So. Oak St., Suite 203, Champaign IL 61820 >>>> 217.531.6112 >>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>> >>>> >>>> >>>> On Jun 20, 2013, at 9:40 AM, Michael Jackson wrote: >>>> >>>> I have built HDF5 1.8.11 on Ubuntu Linux x64 12.04 using static >>>> libraries. I am now trying to compile my program against this build and I >>>> am getting the following errors: >>>> >>>> >>>> make[1]: *** Waiting for unfinished jobs.... >>>> /home/mjackson/DREAM3D_SDK/hdf5-1.8.11/lib/libhdf5.a(H5PL.c.o): In >>>> function `H5PL_term_interface': >>>> H5PL.c:(.text+0x9d): undefined reference to `dlclose' >>>> /home/mjackson/DREAM3D_SDK/hdf5-1.8.11/lib/libhdf5.a(H5PL.c.o): In >>>> function `H5PL_load': >>>> H5PL.c:(.text+0x2a5): undefined reference to `dlsym' >>>> H5PL.c:(.text+0x38c): undefined reference to `dlopen' >>>> H5PL.c:(.text+0x3a5): undefined reference to `dlsym' >>>> H5PL.c:(.text+0x4d4): undefined reference to `dlclose' >>>> H5PL.c:(.text+0x551): undefined reference to `dlerror' >>>> H5PL.c:(.text+0x745): undefined reference to `dlclose' >>>> collect2: ld returned 1 exit status >>>> make[2]: *** [Bin/H5UtilitiesTest] Error 1 >>>> >>>> I have to admit my C++ Error Fu is not strong today and I am missing >>>> what is wrong. I don't remember having this issue on other systems where I >>>> have HDF5 built as a static library. >>>> >>>> ... 3 Minutes later on Google..... >>>> >>>> >>>> http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg11875.html >>>> >>>> So just as a reminder for those affected that we may need to update our >>>> CMake/M4/Configure scripts to deal with the new features of HDF5 1.8.11 >>>> >>>> Thanks >>>> ___________________________________________________________ >>>> Mike Jackson Principal Software Engineer >>>> BlueQuartz Software Dayton, Ohio >>>> [email protected] www.bluequartz.net >>>> >>>> >>>> _______________________________________________ >>>> Hdf-forum is for HDF software users discussion. >>>> [email protected] >>>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >>>> >>>> >>>> >>>> _______________________________________________ >>>> Hdf-forum is for HDF software users discussion. >>>> [email protected] >>>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >>>> >>> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> [email protected] >> >> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >> >> >> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> [email protected] >> >> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >> >> > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > >
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