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
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 <friesz@usc.edu> 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.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
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 <clipp2@illinois.edu> 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 ClippOn Mon, Nov 21, 2016 at 9:15 PM, Aaron Friesz <friesz@usc.edu> 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.
Hdf-forum@lists.hdfgroup.org
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
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8lJd0EDrmVR3kT_2giZR-JX-it2X2aCkag&e=
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sTb4Ix6jLKp05hJeTt-gGsS_zh4tAnbNmBtQ6VQLNo&e=
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" <friesz@usc.edu> 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)
-lhdf5So 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 <clipp2@illinois.edu> 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 ClippOn Mon, Nov 21, 2016 at 9:15 PM, Aaron Friesz <friesz@usc.edu> 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.
Hdf-forum@lists.hdfgroup.org
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.
Hdf-forum@lists.hdfgroup.org
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_
wYitdnLxg&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.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
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 <clipp2@illinois.edu> 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,
LandonOn Nov 22, 2016 7:13 PM, "Aaron Friesz" <friesz@usc.edu> 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)
-lhdf5So 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 <clipp2@illinois.edu> >> 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 ClippOn Mon, Nov 21, 2016 at 9:15 PM, Aaron Friesz <friesz@usc.edu> 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.
Hdf-forum@lists.hdfgroup.org
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.
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Hdf-forum is for HDF software users discussion.
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--
Aaron Friesz
-----------------------------------------------------
University of Southern California
Department of Electrical Engineering
MicroPhotonic Devices Group
213 740 9208
friesz@usc.edu
