I just wanted to provide an update, in case anyone else has a similar issue.
The system I work on was updated and after the update, during linking of my program, I was getting 'undefined reference' errors for definitions that had specifically to do with parallel file I/O. The issue was that there was a 'hidden' installation of hdf5 in my library path. This installation didn't exist on the system before the update and it was not a parallel library. So, to make a long story short, if you get 'undefined reference' for something you are certain should be in your library, go hunting in your library path for a rogue install of the same library. Aaron On Tue, Nov 22, 2016 at 6:34 PM, Landon Clipp <[email protected]> wrote: > Without having access to your computer, it's difficult to tell exactly > what is going on so I just need to give you maybe the insultingly obvious > answers. You of course you want to check the paths to make sure all lib and > include files are actually present. You might want to ask your system > administrator to reinstall HDF libraries. I see you are doing dynamic > linking, it is possible like you said that for some reason or another your > libraries were not compiled. If that's truly the case, the only way to fix > it is to recompile the libraries. That would have to be a question for your > admin. > > Sorry if this isn't terribly helpful, this issue isn't easily resolved > without access to and familiarity with the system. I've dealt with > undefined reference problems a lot and it always seems to be a different > issue, but it of course is a symptom of the linker being unable to find the > proper libraries or a botched installation of the libraries. My main advice > would be to just make sure the libraries are in the directory you are > telling the compiler they're at, or if your system has two versions of the > HDF libraries and you're using the older one. > > Another thing that I thought may be causing issues, I'm not familiar with > mpicxx but I assume this is a gcc wrapper of some kind. I know at least > with h4cc and h5cc, they are configured to include the hdf libraries upon > install and if you move the library, h4cc/h5cc will be pointing to nothing > and thus fail to include the library. I'm curious if mpicxx has a verbose > compilation flag that would let you see what commands/flags it is giving to > your native compiler. > > Regards, > Landon > > On Nov 22, 2016 7:13 PM, "Aaron Friesz" <[email protected]> wrote: > >> That is exactly what is happening. Unfortunately I'm not certain of all >> the details as I don't maintain the install that is provided on the >> system. I used to maintain my own version, but when the system was updated >> to BeeGFS it became easier to use the one provided. >> >> In terms of the specific linker call, in a simplified form, it looks like >> >> mpicxx (object file list) (other libraries) -L(location of libhdf5.so) >> -lhdf5 >> >> So far as I can tell, the only undefined references are those that >> include H5P, I'm suspecting that they did not recompile the parallel >> version of the libraries. >> >> On Tue, Nov 22, 2016 at 1:08 PM, Landon Clipp <[email protected]> >> wrote: >> >>> Aaron, >>> >>> Undefined references almost always mean that your compiler is not >>> linking the libraries you need. This is not surprising considering your >>> machine was recently upgraded. A little bit more information about your >>> environment, compilation procedures etc would be helpful to determine why >>> your libraries are not being properly included. >>> >>> Regards, >>> Landon Clipp >>> >>> On Mon, Nov 21, 2016 at 9:15 PM, Aaron Friesz <[email protected]> wrote: >>> >>>> The machine I work on was recently upgraded. When I compile against >>>> the HDF5 libraries that are installed on the system (1.18), I get these >>>> errors when trying to link. Any help with figuring out what is wrong would >>>> be greatly appreciated. >>>> >>>> -- >>>> Aaron Friesz >>>> >>>> >>>> _______________________________________________ >>>> Hdf-forum is for HDF software users discussion. >>>> [email protected] >>>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.hdfgroup.org_mailman_listinfo_hdf-2Dforum-5Flists.hdfgroup.org&d=DgMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx9txIqgEINHtVDIDfXdIw&m=aqPxJiCbdUQL5Kxkl4EOchQYc5_Apm8gW_wYitdnLxg&s=MgsqMuu5_8lJd0EDrmVR3kT_2giZR-JX-it2X2aCkag&e=> >>>> Twitter: https://twitter.com/hdf5 >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_hdf5&d=DgMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx9txIqgEINHtVDIDfXdIw&m=aqPxJiCbdUQL5Kxkl4EOchQYc5_Apm8gW_wYitdnLxg&s=-sTb4Ix6jLKp05hJeTt-gGsS_zh4tAnbNmBtQ6VQLNo&e=> >>>> >>> >>> >>> _______________________________________________ >>> Hdf-forum is for HDF software users discussion. >>> [email protected] >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.hd >>> fgroup.org_mailman_listinfo_hdf-2Dforum-5Flists.hdfgroup.org >>> &d=DgICAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx >>> 9txIqgEINHtVDIDfXdIw&m=aqPxJiCbdUQL5Kxkl4EOchQYc5_Apm8gW_wYi >>> tdnLxg&s=MgsqMuu5_8lJd0EDrmVR3kT_2giZR-JX-it2X2aCkag&e= >>> Twitter: https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter >>> .com_hdf5&d=DgICAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfn >>> c_gI&r=Rx9txIqgEINHtVDIDfXdIw&m=aqPxJiCbdUQL5Kxkl4EOchQYc5_A >>> pm8gW_wYitdnLxg&s=-sTb4Ix6jLKp05hJeTt-gGsS_zh4tAnbNmBtQ6VQLNo&e= >>> >> >> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> [email protected] >> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.hdfgroup.org_mailman_listinfo_hdf-2Dforum-5Flists.hdfgroup.org&d=DgMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx9txIqgEINHtVDIDfXdIw&m=7f4y0yurnqUfMPjJp6M4FJSE1u1BKk325rUMEf4MYt0&s=aoQyt_zxzDEcCowCiF9QpFItGpcNXp4PWbdjIg76HXg&e=> >> Twitter: https://twitter.com/hdf5 >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_hdf5&d=DgMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx9txIqgEINHtVDIDfXdIw&m=7f4y0yurnqUfMPjJp6M4FJSE1u1BKk325rUMEf4MYt0&s=I6JEOLD8U_pf2hnO0PWObLdEaLEGmof8Moevbx3tTzc&e=> >> > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists. > hdfgroup.org_mailman_listinfo_hdf-2Dforum-5Flists.hdfgroup.org&d=DgICAg&c= > clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Rx9txIqgEINHtVDIDfXdIw&m= > 7f4y0yurnqUfMPjJp6M4FJSE1u1BKk325rUMEf4MYt0&s=aoQyt_ > zxzDEcCowCiF9QpFItGpcNXp4PWbdjIg76HXg&e= > Twitter: https://urldefense.proofpoint.com/v2/url?u=https-3A__ > twitter.com_hdf5&d=DgICAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r= > Rx9txIqgEINHtVDIDfXdIw&m=7f4y0yurnqUfMPjJp6M4FJSE1u1BKk > 325rUMEf4MYt0&s=I6JEOLD8U_pf2hnO0PWObLdEaLEGmof8Moevbx3tTzc&e= > -- Aaron Friesz ----------------------------------------------------- University of Southern California Department of Electrical Engineering MicroPhotonic Devices Group 213 740 9208 [email protected]
_______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
