From ondrej.certik at gmail.com Tue Feb 24 17:52:44 2015 From: ondrej.certik at gmail.com (=?UTF-8?B?T25kxZllaiDEjGVydMOtaw==?=) Date: Tue, 24 Feb 2015 15:52:44 -0700 Subject: [Cmb-users] CMB binary doesn't work on my RHEL6 Message-ID: Hi, As I mentioned during the call to Andy, I wanted to try CMB, so I went here: http://www.computationalmodelbuilder.org/download/ and did: $ wget http://www.computationalmodelbuilder.org/files/CMBSuite-3.0.0-Linux-x86_64.tar.gz $ tar xaf CMBSuite-3.0.0-Linux-x86_64.tar.gz $ cd CMBSuite-3.0.0-Linux-x86_64 $ ./bin/MeshViewer /tmp/CMBSuite-3.0.0-Linux-x86_64/lib/cmb-3.0/MeshViewer: error while loading shared libraries: libcurl.so.3: cannot open shared object file: No such file or directory I have libcurl.so.4 here: $ ls /usr/lib/libcurl.so.* /usr/lib/libcurl.so.4 /usr/lib/libcurl.so.4.1.1 But not 3. I think you should ship the required libraries like libcurl.so.3 in lib/cmb-3.0/. Ondrej From andy.bauer at kitware.com Tue Feb 24 21:28:02 2015 From: andy.bauer at kitware.com (Andy Bauer) Date: Tue, 24 Feb 2015 21:28:02 -0500 Subject: [Cmb-users] CMB binary doesn't work on my RHEL6 In-Reply-To: References: Message-ID: Hi Ondrej, You're not the first to hit this issue. I still appreciate the report though. The other user hacked around this by putting in a link from /usr/lib/libcurl.so.3 to /usr/lib/libcurl.so.4. It's not a satisfying fix but if you're eager to try CMB out it should get you going. I'll push for a fix in the next installer we make for CMB. Regards, Andy On Tue, Feb 24, 2015 at 5:52 PM, Ond?ej ?ert?k wrote: > Hi, > > As I mentioned during the call to Andy, I wanted to try CMB, so I went > here: > > http://www.computationalmodelbuilder.org/download/ > > and did: > > $ wget > http://www.computationalmodelbuilder.org/files/CMBSuite-3.0.0-Linux-x86_64.tar.gz > $ tar xaf CMBSuite-3.0.0-Linux-x86_64.tar.gz > $ cd CMBSuite-3.0.0-Linux-x86_64 > $ ./bin/MeshViewer > /tmp/CMBSuite-3.0.0-Linux-x86_64/lib/cmb-3.0/MeshViewer: error while > loading shared libraries: libcurl.so.3: cannot open shared object > file: No such file or directory > > I have libcurl.so.4 here: > > $ ls /usr/lib/libcurl.so.* > /usr/lib/libcurl.so.4 /usr/lib/libcurl.so.4.1.1 > > But not 3. I think you should ship the required libraries like > libcurl.so.3 in lib/cmb-3.0/. > > Ondrej > _______________________________________________ > Cmb-users mailing list > Cmb-users at computationalmodelbuilder.org > http://public.kitware.com/mailman/listinfo/cmb-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bob.obara at kitware.com Tue Feb 24 21:45:23 2015 From: bob.obara at kitware.com (Robert Michael O'Bara) Date: Tue, 24 Feb 2015 21:45:23 -0500 Subject: [Cmb-users] CMB binary doesn't work on my RHEL6 In-Reply-To: References: Message-ID: <30EF134D-7567-4A22-BEAF-0EB291E02DC9@kitware.com> I Believe that this has been fixed in the latest superbuild since CMB doesn?t use curl. Bob Robert M. O'Bara, MEng. Assistant Director of Scientific Computing Kitware Inc. 28 Corporate Drive Suite 101 Clifton Park, NY 12065 Phone: (518) 881- 4931 > On Feb 24, 2015, at 9:28 PM, Andy Bauer wrote: > > Hi Ondrej, > > You're not the first to hit this issue. I still appreciate the report though. The other user hacked around this by putting in a link from /usr/lib/libcurl.so.3 to /usr/lib/libcurl.so.4. It's not a satisfying fix but if you're eager to try CMB out it should get you going. > > I'll push for a fix in the next installer we make for CMB. > > Regards, > Andy > > On Tue, Feb 24, 2015 at 5:52 PM, Ond?ej ?ert?k > wrote: > Hi, > > As I mentioned during the call to Andy, I wanted to try CMB, so I went here: > > http://www.computationalmodelbuilder.org/download/ > > and did: > > $ wget http://www.computationalmodelbuilder.org/files/CMBSuite-3.0.0-Linux-x86_64.tar.gz > $ tar xaf CMBSuite-3.0.0-Linux-x86_64.tar.gz > $ cd CMBSuite-3.0.0-Linux-x86_64 > $ ./bin/MeshViewer > /tmp/CMBSuite-3.0.0-Linux-x86_64/lib/cmb-3.0/MeshViewer: error while > loading shared libraries: libcurl.so.3: cannot open shared object > file: No such file or directory > > I have libcurl.so.4 here: > > $ ls /usr/lib/libcurl.so.* > /usr/lib/libcurl.so.4 /usr/lib/libcurl.so.4.1.1 > > But not 3. I think you should ship the required libraries like > libcurl.so.3 in lib/cmb-3.0/. > > Ondrej > _______________________________________________ > Cmb-users mailing list > Cmb-users at computationalmodelbuilder.org > http://public.kitware.com/mailman/listinfo/cmb-users > > _______________________________________________ > Cmb-users mailing list > Cmb-users at computationalmodelbuilder.org > http://public.kitware.com/mailman/listinfo/cmb-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From robert.maynard at kitware.com Wed Feb 25 08:45:57 2015 From: robert.maynard at kitware.com (Robert Maynard) Date: Wed, 25 Feb 2015 08:45:57 -0500 Subject: [Cmb-users] CMB binary doesn't work on my RHEL6 In-Reply-To: <30EF134D-7567-4A22-BEAF-0EB291E02DC9@kitware.com> References: <30EF134D-7567-4A22-BEAF-0EB291E02DC9@kitware.com> Message-ID: Hi, I believe the issue was tracked down to be caused by netcdf dap support which implicitly used system libcurl without our knowledge. To re-iterate what Bob said, we have fixed the issue and going forward we won't link to libcurl. On Tue, Feb 24, 2015 at 9:45 PM, Robert Michael O'Bara wrote: > I Believe that this has been fixed in the latest superbuild since CMB > doesn?t use curl. > > Bob > > Robert M. O'Bara, MEng. > Assistant Director of Scientific Computing > > Kitware Inc. > 28 Corporate Drive > Suite 101 > Clifton Park, NY 12065 > > Phone: (518) 881- 4931 > > > > > On Feb 24, 2015, at 9:28 PM, Andy Bauer wrote: > > Hi Ondrej, > > You're not the first to hit this issue. I still appreciate the report > though. The other user hacked around this by putting in a link from > /usr/lib/libcurl.so.3 to /usr/lib/libcurl.so.4. It's not a satisfying fix > but if you're eager to try CMB out it should get you going. > > I'll push for a fix in the next installer we make for CMB. > > Regards, > Andy > > On Tue, Feb 24, 2015 at 5:52 PM, Ond?ej ?ert?k > wrote: >> >> Hi, >> >> As I mentioned during the call to Andy, I wanted to try CMB, so I went >> here: >> >> http://www.computationalmodelbuilder.org/download/ >> >> and did: >> >> $ wget >> http://www.computationalmodelbuilder.org/files/CMBSuite-3.0.0-Linux-x86_64.tar.gz >> $ tar xaf CMBSuite-3.0.0-Linux-x86_64.tar.gz >> $ cd CMBSuite-3.0.0-Linux-x86_64 >> $ ./bin/MeshViewer >> /tmp/CMBSuite-3.0.0-Linux-x86_64/lib/cmb-3.0/MeshViewer: error while >> loading shared libraries: libcurl.so.3: cannot open shared object >> file: No such file or directory >> >> I have libcurl.so.4 here: >> >> $ ls /usr/lib/libcurl.so.* >> /usr/lib/libcurl.so.4 /usr/lib/libcurl.so.4.1.1 >> >> But not 3. I think you should ship the required libraries like >> libcurl.so.3 in lib/cmb-3.0/. >> >> Ondrej >> _______________________________________________ >> Cmb-users mailing list >> Cmb-users at computationalmodelbuilder.org >> http://public.kitware.com/mailman/listinfo/cmb-users > > > _______________________________________________ > Cmb-users mailing list > Cmb-users at computationalmodelbuilder.org > http://public.kitware.com/mailman/listinfo/cmb-users > > > > _______________________________________________ > Cmb-users mailing list > Cmb-users at computationalmodelbuilder.org > http://public.kitware.com/mailman/listinfo/cmb-users > From ondrej.certik at gmail.com Wed Feb 25 12:29:03 2015 From: ondrej.certik at gmail.com (=?UTF-8?B?T25kxZllaiDEjGVydMOtaw==?=) Date: Wed, 25 Feb 2015 10:29:03 -0700 Subject: [Cmb-users] CMB binary doesn't work on my RHEL6 In-Reply-To: References: <30EF134D-7567-4A22-BEAF-0EB291E02DC9@kitware.com> Message-ID: Hi Andy, Robert and Robert, Thanks for the replies. Do you know when you will upload a new binary? In the meantime I tried to compile from source using https://github.com/Kitware/RGG. Once I figure this out, I'll add it to Hashdist (https://hashdist.github.io/). We actually have pretty much all the dependencies, except perhaps Remus, I'll add it in. Is my understanding correct, that if I want to use the superbuild (as a temporary solution before I add all the dependencies to Hashdist), I first do: cd superbuild cmake . make Do I need to install it afterwards and then somehow point the cmake to it from the root directory? Once I understand that, I'll be happy to improve the README with some instructions. Ondrej On Wed, Feb 25, 2015 at 6:45 AM, Robert Maynard wrote: > Hi, > > I believe the issue was tracked down to be caused by netcdf dap > support which implicitly used system libcurl without our knowledge. To > re-iterate what Bob said, we have fixed the issue and going forward we > won't link to libcurl. > > On Tue, Feb 24, 2015 at 9:45 PM, Robert Michael O'Bara > wrote: >> I Believe that this has been fixed in the latest superbuild since CMB >> doesn?t use curl. >> >> Bob >> >> Robert M. O'Bara, MEng. >> Assistant Director of Scientific Computing >> >> Kitware Inc. >> 28 Corporate Drive >> Suite 101 >> Clifton Park, NY 12065 >> >> Phone: (518) 881- 4931 >> >> >> >> >> On Feb 24, 2015, at 9:28 PM, Andy Bauer wrote: >> >> Hi Ondrej, >> >> You're not the first to hit this issue. I still appreciate the report >> though. The other user hacked around this by putting in a link from >> /usr/lib/libcurl.so.3 to /usr/lib/libcurl.so.4. It's not a satisfying fix >> but if you're eager to try CMB out it should get you going. >> >> I'll push for a fix in the next installer we make for CMB. >> >> Regards, >> Andy >> >> On Tue, Feb 24, 2015 at 5:52 PM, Ond?ej ?ert?k >> wrote: >>> >>> Hi, >>> >>> As I mentioned during the call to Andy, I wanted to try CMB, so I went >>> here: >>> >>> http://www.computationalmodelbuilder.org/download/ >>> >>> and did: >>> >>> $ wget >>> http://www.computationalmodelbuilder.org/files/CMBSuite-3.0.0-Linux-x86_64.tar.gz >>> $ tar xaf CMBSuite-3.0.0-Linux-x86_64.tar.gz >>> $ cd CMBSuite-3.0.0-Linux-x86_64 >>> $ ./bin/MeshViewer >>> /tmp/CMBSuite-3.0.0-Linux-x86_64/lib/cmb-3.0/MeshViewer: error while >>> loading shared libraries: libcurl.so.3: cannot open shared object >>> file: No such file or directory >>> >>> I have libcurl.so.4 here: >>> >>> $ ls /usr/lib/libcurl.so.* >>> /usr/lib/libcurl.so.4 /usr/lib/libcurl.so.4.1.1 >>> >>> But not 3. I think you should ship the required libraries like >>> libcurl.so.3 in lib/cmb-3.0/. >>> >>> Ondrej >>> _______________________________________________ >>> Cmb-users mailing list >>> Cmb-users at computationalmodelbuilder.org >>> http://public.kitware.com/mailman/listinfo/cmb-users >> >> >> _______________________________________________ >> Cmb-users mailing list >> Cmb-users at computationalmodelbuilder.org >> http://public.kitware.com/mailman/listinfo/cmb-users >> >> >> >> _______________________________________________ >> Cmb-users mailing list >> Cmb-users at computationalmodelbuilder.org >> http://public.kitware.com/mailman/listinfo/cmb-users >> > _______________________________________________ > Cmb-users mailing list > Cmb-users at computationalmodelbuilder.org > http://public.kitware.com/mailman/listinfo/cmb-users From robert.maynard at kitware.com Wed Feb 25 12:36:50 2015 From: robert.maynard at kitware.com (Robert Maynard) Date: Wed, 25 Feb 2015 12:36:50 -0500 Subject: [Cmb-users] CMB binary doesn't work on my RHEL6 In-Reply-To: References: <30EF134D-7567-4A22-BEAF-0EB291E02DC9@kitware.com> Message-ID: On Wed, Feb 25, 2015 at 12:29 PM, Ond?ej ?ert?k wrote: > Hi Andy, Robert and Robert, > > Thanks for the replies. Do you know when you will upload a new binary? > > In the meantime I tried to compile from source using > https://github.com/Kitware/RGG. > Once I figure this out, I'll add it to Hashdist > (https://hashdist.github.io/). We actually have pretty much all the > dependencies, except perhaps Remus, I'll add it in. Last year I wrote a hashstack recipe for most of cmb which can be found at https://github.com/robertmaynard/hashstack/tree/cmb-profile/ , it does include Remus. > > Is my understanding correct, that if I want to use the superbuild (as > a temporary solution before I add all the dependencies to Hashdist), I > first do: > > cd superbuild > cmake . > make > > Do I need to install it afterwards and then somehow point the cmake to > it from the root directory? Once I understand that, I'll be happy to > improve the README with some instructions. Basically that is correct, but the superbuild will install everything into /install/ (include/lib/bin). So you should be able to add /install as a CMAKE_PREFIX_PATH to find anything it has built. > > > Ondrej > > On Wed, Feb 25, 2015 at 6:45 AM, Robert Maynard > wrote: >> Hi, >> >> I believe the issue was tracked down to be caused by netcdf dap >> support which implicitly used system libcurl without our knowledge. To >> re-iterate what Bob said, we have fixed the issue and going forward we >> won't link to libcurl. >> >> On Tue, Feb 24, 2015 at 9:45 PM, Robert Michael O'Bara >> wrote: >>> I Believe that this has been fixed in the latest superbuild since CMB >>> doesn?t use curl. >>> >>> Bob >>> >>> Robert M. O'Bara, MEng. >>> Assistant Director of Scientific Computing >>> >>> Kitware Inc. >>> 28 Corporate Drive >>> Suite 101 >>> Clifton Park, NY 12065 >>> >>> Phone: (518) 881- 4931 >>> >>> >>> >>> >>> On Feb 24, 2015, at 9:28 PM, Andy Bauer wrote: >>> >>> Hi Ondrej, >>> >>> You're not the first to hit this issue. I still appreciate the report >>> though. The other user hacked around this by putting in a link from >>> /usr/lib/libcurl.so.3 to /usr/lib/libcurl.so.4. It's not a satisfying fix >>> but if you're eager to try CMB out it should get you going. >>> >>> I'll push for a fix in the next installer we make for CMB. >>> >>> Regards, >>> Andy >>> >>> On Tue, Feb 24, 2015 at 5:52 PM, Ond?ej ?ert?k >>> wrote: >>>> >>>> Hi, >>>> >>>> As I mentioned during the call to Andy, I wanted to try CMB, so I went >>>> here: >>>> >>>> http://www.computationalmodelbuilder.org/download/ >>>> >>>> and did: >>>> >>>> $ wget >>>> http://www.computationalmodelbuilder.org/files/CMBSuite-3.0.0-Linux-x86_64.tar.gz >>>> $ tar xaf CMBSuite-3.0.0-Linux-x86_64.tar.gz >>>> $ cd CMBSuite-3.0.0-Linux-x86_64 >>>> $ ./bin/MeshViewer >>>> /tmp/CMBSuite-3.0.0-Linux-x86_64/lib/cmb-3.0/MeshViewer: error while >>>> loading shared libraries: libcurl.so.3: cannot open shared object >>>> file: No such file or directory >>>> >>>> I have libcurl.so.4 here: >>>> >>>> $ ls /usr/lib/libcurl.so.* >>>> /usr/lib/libcurl.so.4 /usr/lib/libcurl.so.4.1.1 >>>> >>>> But not 3. I think you should ship the required libraries like >>>> libcurl.so.3 in lib/cmb-3.0/. >>>> >>>> Ondrej >>>> _______________________________________________ >>>> Cmb-users mailing list >>>> Cmb-users at computationalmodelbuilder.org >>>> http://public.kitware.com/mailman/listinfo/cmb-users >>> >>> >>> _______________________________________________ >>> Cmb-users mailing list >>> Cmb-users at computationalmodelbuilder.org >>> http://public.kitware.com/mailman/listinfo/cmb-users >>> >>> >>> >>> _______________________________________________ >>> Cmb-users mailing list >>> Cmb-users at computationalmodelbuilder.org >>> http://public.kitware.com/mailman/listinfo/cmb-users >>> >> _______________________________________________ >> Cmb-users mailing list >> Cmb-users at computationalmodelbuilder.org >> http://public.kitware.com/mailman/listinfo/cmb-users From ondrej.certik at gmail.com Wed Feb 25 12:54:41 2015 From: ondrej.certik at gmail.com (=?UTF-8?B?T25kxZllaiDEjGVydMOtaw==?=) Date: Wed, 25 Feb 2015 10:54:41 -0700 Subject: [Cmb-users] CMB binary doesn't work on my RHEL6 In-Reply-To: References: <30EF134D-7567-4A22-BEAF-0EB291E02DC9@kitware.com> Message-ID: On Wed, Feb 25, 2015 at 10:36 AM, Robert Maynard wrote: > On Wed, Feb 25, 2015 at 12:29 PM, Ond?ej ?ert?k wrote: >> Hi Andy, Robert and Robert, >> >> Thanks for the replies. Do you know when you will upload a new binary? >> >> In the meantime I tried to compile from source using >> https://github.com/Kitware/RGG. >> Once I figure this out, I'll add it to Hashdist >> (https://hashdist.github.io/). We actually have pretty much all the >> dependencies, except perhaps Remus, I'll add it in. > > Last year I wrote a hashstack recipe for most of cmb which can be > found at https://github.com/robertmaynard/hashstack/tree/cmb-profile/ > , it does include Remus. I didn't know! Can I create a pull request from your branch? > >> >> Is my understanding correct, that if I want to use the superbuild (as >> a temporary solution before I add all the dependencies to Hashdist), I >> first do: >> >> cd superbuild >> cmake . >> make >> >> Do I need to install it afterwards and then somehow point the cmake to >> it from the root directory? Once I understand that, I'll be happy to >> improve the README with some instructions. > > Basically that is correct, but the superbuild will install everything > into /install/ (include/lib/bin). > So you should be able to add /install as a > CMAKE_PREFIX_PATH to find anything it has built. Ah I see, right. So it built a few packages and then failed with: -- Up-to-date: /local/certik/repos/RGG/superbuild/install/lib/cmake/qttesting/QtTestingTargets.cmake -- Installing: /local/certik/repos/RGG/superbuild/install/lib/cmake/qttesting/QtTestingTargets-noconfig.cmake [ 40%] Completed 'QtTesting' [ 42%] Built target QtTesting [ 48%] Built target boost [ 54%] Built target szip [ 60%] Built target hdf5 [ 60%] Performing configure step for 'netcdf' Not searching for unused variables given on the command line. CMake Warning (dev) in CMakeLists.txt: Syntax Warning in cmake code at /local/certik/repos/RGG/superbuild/netcdf/src/netcdf/CMakeLists.txt:339:56 Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:78 (FIND_PACKAGE): Syntax Warning in cmake code at /local/certik/repos/RGG/superbuild/netcdf/src/netcdf/cmake/modules/FindMakeDist.cmake:202:40 Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find CURL (missing: CURL_LIBRARY CURL_INCLUDE_DIR) CMake Error at CMakeLists.txt:425 (MESSAGE): DAP Support specified, CURL libraries are not found. -- Configuring incomplete, errors occurred! See also "/local/certik/repos/RGG/superbuild/netcdf/src/netcdf-build/CMakeFiles/CMakeOutput.log". See also "/local/certik/repos/RGG/superbuild/netcdf/src/netcdf-build/CMakeFiles/CMakeError.log". make[2]: *** [netcdf/src/netcdf-stamp/netcdf-configure] Error 1 make[1]: *** [CMakeFiles/netcdf.dir/all] Error 2 make: *** [all] Error 2 It failed with Curl. I'll move over to your branch now, I know how to fix such problems in there if needed. Ondrej From robert.maynard at kitware.com Wed Feb 25 13:06:36 2015 From: robert.maynard at kitware.com (Robert Maynard) Date: Wed, 25 Feb 2015 13:06:36 -0500 Subject: [Cmb-users] CMB binary doesn't work on my RHEL6 In-Reply-To: References: <30EF134D-7567-4A22-BEAF-0EB291E02DC9@kitware.com> Message-ID: On Wed, Feb 25, 2015 at 12:54 PM, Ond?ej ?ert?k wrote: > On Wed, Feb 25, 2015 at 10:36 AM, Robert Maynard > wrote: >> On Wed, Feb 25, 2015 at 12:29 PM, Ond?ej ?ert?k wrote: >>> Hi Andy, Robert and Robert, >>> >>> Thanks for the replies. Do you know when you will upload a new binary? >>> >>> In the meantime I tried to compile from source using >>> https://github.com/Kitware/RGG. >>> Once I figure this out, I'll add it to Hashdist >>> (https://hashdist.github.io/). We actually have pretty much all the >>> dependencies, except perhaps Remus, I'll add it in. >> >> Last year I wrote a hashstack recipe for most of cmb which can be >> found at https://github.com/robertmaynard/hashstack/tree/cmb-profile/ >> , it does include Remus. > > I didn't know! Can I create a pull request from your branch? I am hesitant to do a pull request as the branch is pretty old and the version of our dependencies might be out of date in that branch. We should review the packages that the branch adds and verify they are using the same version as the SuperBuild versions.cmake > >> >>> >>> Is my understanding correct, that if I want to use the superbuild (as >>> a temporary solution before I add all the dependencies to Hashdist), I >>> first do: >>> >>> cd superbuild >>> cmake . >>> make >>> >>> Do I need to install it afterwards and then somehow point the cmake to >>> it from the root directory? Once I understand that, I'll be happy to >>> improve the README with some instructions. >> >> Basically that is correct, but the superbuild will install everything >> into /install/ (include/lib/bin). >> So you should be able to add /install as a >> CMAKE_PREFIX_PATH to find anything it has built. > > Ah I see, right. So it built a few packages and then failed with: > > -- Up-to-date: /local/certik/repos/RGG/superbuild/install/lib/cmake/qttesting/QtTestingTargets.cmake > -- Installing: /local/certik/repos/RGG/superbuild/install/lib/cmake/qttesting/QtTestingTargets-noconfig.cmake > [ 40%] Completed 'QtTesting' > [ 42%] Built target QtTesting > [ 48%] Built target boost > [ 54%] Built target szip > [ 60%] Built target hdf5 > [ 60%] Performing configure step for 'netcdf' > Not searching for unused variables given on the command line. > CMake Warning (dev) in CMakeLists.txt: > Syntax Warning in cmake code at > > /local/certik/repos/RGG/superbuild/netcdf/src/netcdf/CMakeLists.txt:339:56 > > Argument not separated from preceding token by whitespace. > This warning is for project developers. Use -Wno-dev to suppress it. > > CMake Warning (dev) at CMakeLists.txt:78 (FIND_PACKAGE): > Syntax Warning in cmake code at > > /local/certik/repos/RGG/superbuild/netcdf/src/netcdf/cmake/modules/FindMakeDist.cmake:202:40 > > Argument not separated from preceding token by whitespace. > This warning is for project developers. Use -Wno-dev to suppress it. > > -- Could NOT find CURL (missing: CURL_LIBRARY CURL_INCLUDE_DIR) > CMake Error at CMakeLists.txt:425 (MESSAGE): > DAP Support specified, CURL libraries are not found. > > > -- Configuring incomplete, errors occurred! > See also "/local/certik/repos/RGG/superbuild/netcdf/src/netcdf-build/CMakeFiles/CMakeOutput.log". > See also "/local/certik/repos/RGG/superbuild/netcdf/src/netcdf-build/CMakeFiles/CMakeError.log". > make[2]: *** [netcdf/src/netcdf-stamp/netcdf-configure] Error 1 > make[1]: *** [CMakeFiles/netcdf.dir/all] Error 2 > make: *** [all] Error 2 > > > > > > It failed with Curl. I'll move over to your branch now, I know how to > fix such problems in there if needed. > FYI the cmb superbuild and the RGG superbuild are actually different projects. If you are building RGG I would stick with that superbuild as the dependencies differ. It looks like the CMB superbuild has the fixes for disabling DAP support but that wasn't ported to the RGG superbuild. > Ondrej From ondrej.certik at gmail.com Wed Feb 25 13:14:30 2015 From: ondrej.certik at gmail.com (=?UTF-8?B?T25kxZllaiDEjGVydMOtaw==?=) Date: Wed, 25 Feb 2015 11:14:30 -0700 Subject: [Cmb-users] CMB binary doesn't work on my RHEL6 In-Reply-To: References: <30EF134D-7567-4A22-BEAF-0EB291E02DC9@kitware.com> Message-ID: On Wed, Feb 25, 2015 at 11:06 AM, Robert Maynard wrote: > On Wed, Feb 25, 2015 at 12:54 PM, Ond?ej ?ert?k wrote: >> On Wed, Feb 25, 2015 at 10:36 AM, Robert Maynard >> wrote: >>> On Wed, Feb 25, 2015 at 12:29 PM, Ond?ej ?ert?k wrote: >>>> Hi Andy, Robert and Robert, >>>> >>>> Thanks for the replies. Do you know when you will upload a new binary? >>>> >>>> In the meantime I tried to compile from source using >>>> https://github.com/Kitware/RGG. >>>> Once I figure this out, I'll add it to Hashdist >>>> (https://hashdist.github.io/). We actually have pretty much all the >>>> dependencies, except perhaps Remus, I'll add it in. >>> >>> Last year I wrote a hashstack recipe for most of cmb which can be >>> found at https://github.com/robertmaynard/hashstack/tree/cmb-profile/ >>> , it does include Remus. >> >> I didn't know! Can I create a pull request from your branch? > > I am hesitant to do a pull request as the branch is pretty old and the > version of our > dependencies might be out of date in that branch. We should review the packages > that the branch adds and verify they are using the same version as the > SuperBuild > versions.cmake Ok, I am building your branch now and I'll fix any problems. If it builds and works, I'll send a PR. >>>> Is my understanding correct, that if I want to use the superbuild (as >>>> a temporary solution before I add all the dependencies to Hashdist), I >>>> first do: >>>> >>>> cd superbuild >>>> cmake . >>>> make >>>> >>>> Do I need to install it afterwards and then somehow point the cmake to >>>> it from the root directory? Once I understand that, I'll be happy to >>>> improve the README with some instructions. >>> >>> Basically that is correct, but the superbuild will install everything >>> into /install/ (include/lib/bin). >>> So you should be able to add /install as a >>> CMAKE_PREFIX_PATH to find anything it has built. >> >> Ah I see, right. So it built a few packages and then failed with: >> >> -- Up-to-date: /local/certik/repos/RGG/superbuild/install/lib/cmake/qttesting/QtTestingTargets.cmake >> -- Installing: /local/certik/repos/RGG/superbuild/install/lib/cmake/qttesting/QtTestingTargets-noconfig.cmake >> [ 40%] Completed 'QtTesting' >> [ 42%] Built target QtTesting >> [ 48%] Built target boost >> [ 54%] Built target szip >> [ 60%] Built target hdf5 >> [ 60%] Performing configure step for 'netcdf' >> Not searching for unused variables given on the command line. >> CMake Warning (dev) in CMakeLists.txt: >> Syntax Warning in cmake code at >> >> /local/certik/repos/RGG/superbuild/netcdf/src/netcdf/CMakeLists.txt:339:56 >> >> Argument not separated from preceding token by whitespace. >> This warning is for project developers. Use -Wno-dev to suppress it. >> >> CMake Warning (dev) at CMakeLists.txt:78 (FIND_PACKAGE): >> Syntax Warning in cmake code at >> >> /local/certik/repos/RGG/superbuild/netcdf/src/netcdf/cmake/modules/FindMakeDist.cmake:202:40 >> >> Argument not separated from preceding token by whitespace. >> This warning is for project developers. Use -Wno-dev to suppress it. >> >> -- Could NOT find CURL (missing: CURL_LIBRARY CURL_INCLUDE_DIR) >> CMake Error at CMakeLists.txt:425 (MESSAGE): >> DAP Support specified, CURL libraries are not found. >> >> >> -- Configuring incomplete, errors occurred! >> See also "/local/certik/repos/RGG/superbuild/netcdf/src/netcdf-build/CMakeFiles/CMakeOutput.log". >> See also "/local/certik/repos/RGG/superbuild/netcdf/src/netcdf-build/CMakeFiles/CMakeError.log". >> make[2]: *** [netcdf/src/netcdf-stamp/netcdf-configure] Error 1 >> make[1]: *** [CMakeFiles/netcdf.dir/all] Error 2 >> make: *** [all] Error 2 >> >> >> >> >> >> It failed with Curl. I'll move over to your branch now, I know how to >> fix such problems in there if needed. >> > > FYI the cmb superbuild and the RGG superbuild are actually different > projects. If you are building RGG I would stick with that superbuild > as the dependencies differ. It looks like the CMB superbuild has the > fixes for disabling DAP support but that wasn't ported to the RGG > superbuild. What is the repository for CMB? I went to: http://www.computationalmodelbuilder.org/download/ and it pointed me to: https://github.com/Kitware/RGG But I noticed in your branch that you use git://public.kitware.com/CMB.git. So I am a bit confused which one is the official repository for CMB. Ondrej From ondrej.certik at gmail.com Wed Feb 25 13:54:20 2015 From: ondrej.certik at gmail.com (=?UTF-8?B?T25kxZllaiDEjGVydMOtaw==?=) Date: Wed, 25 Feb 2015 11:54:20 -0700 Subject: [Cmb-users] CMB binary doesn't work on my RHEL6 In-Reply-To: References: <30EF134D-7567-4A22-BEAF-0EB291E02DC9@kitware.com> Message-ID: On Wed, Feb 25, 2015 at 11:14 AM, Ond?ej ?ert?k wrote: > On Wed, Feb 25, 2015 at 11:06 AM, Robert Maynard > wrote: >> On Wed, Feb 25, 2015 at 12:54 PM, Ond?ej ?ert?k wrote: >>> On Wed, Feb 25, 2015 at 10:36 AM, Robert Maynard >>> wrote: >>>> On Wed, Feb 25, 2015 at 12:29 PM, Ond?ej ?ert?k wrote: >>>>> Hi Andy, Robert and Robert, >>>>> >>>>> Thanks for the replies. Do you know when you will upload a new binary? >>>>> >>>>> In the meantime I tried to compile from source using >>>>> https://github.com/Kitware/RGG. >>>>> Once I figure this out, I'll add it to Hashdist >>>>> (https://hashdist.github.io/). We actually have pretty much all the >>>>> dependencies, except perhaps Remus, I'll add it in. >>>> >>>> Last year I wrote a hashstack recipe for most of cmb which can be >>>> found at https://github.com/robertmaynard/hashstack/tree/cmb-profile/ >>>> , it does include Remus. >>> >>> I didn't know! Can I create a pull request from your branch? >> >> I am hesitant to do a pull request as the branch is pretty old and the >> version of our >> dependencies might be out of date in that branch. We should review the packages >> that the branch adds and verify they are using the same version as the >> SuperBuild >> versions.cmake > > Ok, I am building your branch now and I'll fix any problems. If it > builds and works, I'll send a PR. All dependencies built, here is the PR: https://github.com/hashdist/hashstack/pull/676 Ondrej From robert.maynard at kitware.com Wed Feb 25 15:22:03 2015 From: robert.maynard at kitware.com (Robert Maynard) Date: Wed, 25 Feb 2015 15:22:03 -0500 Subject: [Cmb-users] CMB binary doesn't work on my RHEL6 In-Reply-To: References: <30EF134D-7567-4A22-BEAF-0EB291E02DC9@kitware.com> Message-ID: I expect we have a misunderstanding between CMB and RGG and the website download section didn't clarify this. computationalmodelbuilder.org aka CMB hosts two projects. Project one is CMB Suite ( mislabeled on the download page as just CMB ) which is focused on Hydrology. Secondly we have RGG which focuses on reactors. CMBS and RGG have almost the same set of dependencies smtk, vtk, paraview, remus, boost, qt, etc. The primary difference is the resulting domain specific GUI. I believe we have fallen into trying to build CMBS, when you actually want to build RGG. On Wed, Feb 25, 2015 at 1:14 PM, Ond?ej ?ert?k wrote: > On Wed, Feb 25, 2015 at 11:06 AM, Robert Maynard > wrote: >> On Wed, Feb 25, 2015 at 12:54 PM, Ond?ej ?ert?k wrote: >>> On Wed, Feb 25, 2015 at 10:36 AM, Robert Maynard >>> wrote: >>>> On Wed, Feb 25, 2015 at 12:29 PM, Ond?ej ?ert?k wrote: >>>>> Hi Andy, Robert and Robert, >>>>> >>>>> Thanks for the replies. Do you know when you will upload a new binary? >>>>> >>>>> In the meantime I tried to compile from source using >>>>> https://github.com/Kitware/RGG. >>>>> Once I figure this out, I'll add it to Hashdist >>>>> (https://hashdist.github.io/). We actually have pretty much all the >>>>> dependencies, except perhaps Remus, I'll add it in. >>>> >>>> Last year I wrote a hashstack recipe for most of cmb which can be >>>> found at https://github.com/robertmaynard/hashstack/tree/cmb-profile/ >>>> , it does include Remus. >>> >>> I didn't know! Can I create a pull request from your branch? >> >> I am hesitant to do a pull request as the branch is pretty old and the >> version of our >> dependencies might be out of date in that branch. We should review the packages >> that the branch adds and verify they are using the same version as the >> SuperBuild >> versions.cmake > > Ok, I am building your branch now and I'll fix any problems. If it > builds and works, I'll send a PR. > >>>>> Is my understanding correct, that if I want to use the superbuild (as >>>>> a temporary solution before I add all the dependencies to Hashdist), I >>>>> first do: >>>>> >>>>> cd superbuild >>>>> cmake . >>>>> make >>>>> >>>>> Do I need to install it afterwards and then somehow point the cmake to >>>>> it from the root directory? Once I understand that, I'll be happy to >>>>> improve the README with some instructions. >>>> >>>> Basically that is correct, but the superbuild will install everything >>>> into /install/ (include/lib/bin). >>>> So you should be able to add /install as a >>>> CMAKE_PREFIX_PATH to find anything it has built. >>> >>> Ah I see, right. So it built a few packages and then failed with: >>> >>> -- Up-to-date: /local/certik/repos/RGG/superbuild/install/lib/cmake/qttesting/QtTestingTargets.cmake >>> -- Installing: /local/certik/repos/RGG/superbuild/install/lib/cmake/qttesting/QtTestingTargets-noconfig.cmake >>> [ 40%] Completed 'QtTesting' >>> [ 42%] Built target QtTesting >>> [ 48%] Built target boost >>> [ 54%] Built target szip >>> [ 60%] Built target hdf5 >>> [ 60%] Performing configure step for 'netcdf' >>> Not searching for unused variables given on the command line. >>> CMake Warning (dev) in CMakeLists.txt: >>> Syntax Warning in cmake code at >>> >>> /local/certik/repos/RGG/superbuild/netcdf/src/netcdf/CMakeLists.txt:339:56 >>> >>> Argument not separated from preceding token by whitespace. >>> This warning is for project developers. Use -Wno-dev to suppress it. >>> >>> CMake Warning (dev) at CMakeLists.txt:78 (FIND_PACKAGE): >>> Syntax Warning in cmake code at >>> >>> /local/certik/repos/RGG/superbuild/netcdf/src/netcdf/cmake/modules/FindMakeDist.cmake:202:40 >>> >>> Argument not separated from preceding token by whitespace. >>> This warning is for project developers. Use -Wno-dev to suppress it. >>> >>> -- Could NOT find CURL (missing: CURL_LIBRARY CURL_INCLUDE_DIR) >>> CMake Error at CMakeLists.txt:425 (MESSAGE): >>> DAP Support specified, CURL libraries are not found. >>> >>> >>> -- Configuring incomplete, errors occurred! >>> See also "/local/certik/repos/RGG/superbuild/netcdf/src/netcdf-build/CMakeFiles/CMakeOutput.log". >>> See also "/local/certik/repos/RGG/superbuild/netcdf/src/netcdf-build/CMakeFiles/CMakeError.log". >>> make[2]: *** [netcdf/src/netcdf-stamp/netcdf-configure] Error 1 >>> make[1]: *** [CMakeFiles/netcdf.dir/all] Error 2 >>> make: *** [all] Error 2 >>> >>> >>> >>> >>> >>> It failed with Curl. I'll move over to your branch now, I know how to >>> fix such problems in there if needed. >>> >> >> FYI the cmb superbuild and the RGG superbuild are actually different >> projects. If you are building RGG I would stick with that superbuild >> as the dependencies differ. It looks like the CMB superbuild has the >> fixes for disabling DAP support but that wasn't ported to the RGG >> superbuild. > > What is the repository for CMB? I went to: > > http://www.computationalmodelbuilder.org/download/ > > and it pointed me to: https://github.com/Kitware/RGG > > But I noticed in your branch that you use > git://public.kitware.com/CMB.git. So I am a bit confused which one is > the official repository for CMB. > > Ondrej From ondrej.certik at gmail.com Wed Feb 25 15:24:40 2015 From: ondrej.certik at gmail.com (=?UTF-8?B?T25kxZllaiDEjGVydMOtaw==?=) Date: Wed, 25 Feb 2015 13:24:40 -0700 Subject: [Cmb-users] CMB binary doesn't work on my RHEL6 In-Reply-To: References: <30EF134D-7567-4A22-BEAF-0EB291E02DC9@kitware.com> Message-ID: Hi Robert, On Wed, Feb 25, 2015 at 1:22 PM, Robert Maynard wrote: > I expect we have a misunderstanding between CMB and RGG and the > website download section didn't clarify this. > > computationalmodelbuilder.org aka CMB hosts two projects. Project one > is CMB Suite ( mislabeled on the download page as just CMB ) which is > focused on Hydrology. Secondly we have RGG which focuses on reactors. > > CMBS and RGG have almost the same set of dependencies smtk, vtk, > paraview, remus, boost, qt, etc. The primary difference is the > resulting domain specific GUI. > > I believe we have fallen into trying to build CMBS, when you actually > want to build RGG. I see. I think I want to build CMBS, as that is supposed to work with Hydra at LANL. I think I am quite close, just need to figure out the last few technical issues. Ondrej From ondrej.certik at gmail.com Wed Feb 25 16:56:29 2015 From: ondrej.certik at gmail.com (=?UTF-8?B?T25kxZllaiDEjGVydMOtaw==?=) Date: Wed, 25 Feb 2015 14:56:29 -0700 Subject: [Cmb-users] libpng warning: iCCP: known incorrect sRGB profile Message-ID: Hi, I successfully built CMB using Hashdist, here is a PR: https://github.com/hashdist/hashstack/pull/676 (many thanks to Robert Maynard who did the hard work, I just fixed a few failures). When I run the ModelBuilder, I get the following warnings (in a pop up window as well as a command line): $ ModelBuilder libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile I used libpng 1.6.14. My next question is --- what is the best way to learn it, so that I can use it with Hydra? I'll try to make the tutorial announced at: https://plus.google.com/u/0/events/ck3skmk0j3t5hgnavgut79t06o4 Are there some examples that I can try to run? Ondrej