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Hi!
<div class=""><br class="">
</div>
<div class="">The lack of error message is not helpful to assist with debugging. You must try to reproduce the problem on the node then.</div>
<div class=""><br class="">
</div>
<div class="">Try running “git clone <a href="https://itk.org/ITK.git" class="">https://itk.org/ITK.git</a>” and see if it produces more output.</div>
<div class=""><br class="">
</div>
<div class="">The probable problems are there is network restrictions on your cluster node, or that your git version is too old and does not support the https protocol.</div>
<div class=""><br class="">
</div>
<div class="">You could try changing the CMake variable <span style="color: rgb(51, 51, 51); font-family: Consolas, 'Liberation Mono', Menlo, Courier, monospace; white-space: pre; background-color: rgb(255, 255, 255);" class="">SITK_GIT_PROTOCOL</span> from
“https” to “git” [1]. Currently there is not “ExternalData” cache work around for this.</div>
<div class=""><br class="">
</div>
<div class="">HTH,</div>
<div class="">Brad</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="https://github.com/SimpleITK/SimpleITK/blob/master/SuperBuild/External_ITK.cmake#L36" class="">
https://github.com/SimpleITK/SimpleITK/blob/master/SuperBuild/External_ITK.cmake#L36</a></div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Aug 18, 2016, at 12:04 PM, marco giordano <<a href="mailto:marco.giord@gmail.com" class="">marco.giord@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">
<div class="">
<div class="">
<div class="">Thanks a lot for the help, <br class="">
</div>
I downloaded the Cmake binary and now it seems it is able to download, however the build process gets stuck at cloning ITK:
<br class="">
<br class="">
-- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua<br class="">
[ 18%] Completed 'Lua'<br class="">
[ 18%] Built target Lua<br class="">
[ 20%] Creating directories for 'ITK'<br class="">
[ 21%] Performing download step (git clone) for 'ITK'<br class="">
Cloning into 'ITK'...<br class="">
Install the project...<br class="">
-- Install configuration: "Release"<br class="">
-- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua<br class="">
[ 18%] Completed 'Lua'<br class="">
[ 18%] Built target Lua<br class="">
[ 20%] Creating directories for 'ITK'<br class="">
[ 21%] Performing download step (git clone) for 'ITK'<br class="">
Cloning into 'ITK'...<br class="">
<br class="">
</div>
Maybe a wrong link somewhere ?<br class="">
</div>
Regards<br class="">
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">2016-08-18 15:28 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C]
<span dir="ltr" class=""><<a href="mailto:blowekamp@mail.nih.gov" target="_blank" class="">blowekamp@mail.nih.gov</a>></span>:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">And for the lazier there are now CMake binaries for Linux i386 and x86_64.
<div class=""><br class="">
</div>
<div class=""><a href="https://cmake.org/download/" target="_blank" class="">https://cmake.org/download/</a>
<div class="">
<div class="h5"><br class="">
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Aug 18, 2016, at 8:53 AM, Dženan Zukić <<a href="mailto:dzenanz@gmail.com" target="_blank" class="">dzenanz@gmail.com</a>> wrote:</div>
<br class="">
<div class="">
<div dir="ltr" style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" class="">
<div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">
Hi Marco,</div>
<div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">
<br class="">
</div>
<div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">
as Matt said, you can build CMake from source and while configuring it turn CMAKE_USE_OPENSSL on. Then use it or you can even drop it in instead of the system one.</div>
<div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">
<br class="">
</div>
<div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">
Regards,</div>
<div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">
Dženan</div>
</div>
<div class="gmail_extra" style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<br class="">
<div class="gmail_quote">On Thu, Aug 18, 2016 at 6:14 AM, Richard Beare<span class=""> </span><span dir="ltr" class=""><<a href="mailto:richard.beare@gmail.com" target="_blank" class="">richard.beare@gmail.com</a><wbr class="">></span><span class=""> </span>wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr" class="">A related problem, which I've never found a solution for, is that some cluster software (probably the curl library) is built without ssl support at a critical point. You may have the same issue. Maybe the configuration info for curl
will tell you one way or another whether this is the case and you can request a reinstall.</div>
<div class="">
<div class="">
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Thu, Aug 18, 2016 at 7:37 PM, marco giordano<span class=""> </span><span dir="ltr" class=""><<a href="mailto:marco.giord@gmail.com" target="_blank" class="">marco.giord@gmail.<wbr class="">com</a>></span><span class=""> </span>wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr" class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">Hi there,<span class=""> </span><br class="">
</div>
I checked the internet connection on the node and seems fine (I can download with wget the<span class=""> </span><a href="https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" rel="noreferrer" target="_blank" class="">https://midas3.kitware.<wbr class="">com/midas/api/rest?method=<wbr class="">midas.bitstream.download&<wbr class="">checksum=2e115fe26e435e33b0d5c<wbr class="">022e4490567&algorithm=MD5</a>”).<br class="">
<br class="">
</div>
I run the script<span class=""> </span><a href="https://github.com/conda-forge/cmake-feedstock/blob/master/recipe/SSLTest.cmake" rel="noreferrer" target="_blank" class="">SSLTest.cmake</a><span class=""> </span>but it fails (it downloads a LICENSE file but
it is empty):<br class="">
CMake Error at SSLTest.cmake:5 (file):<br class="">
file DOWNLOAD HASH mismatch<br class="">
<br class="">
for file: [/home/mgiordano/code/SimpleIT<wbr class="">K/LICENSE]<br class="">
expected hash: [f8c925402b90f74566f71e64eea7b<wbr class="">b9d83daac69cde71408ffd6c043be6<wbr class="">a4991]<br class="">
actual hash: [e3b0c44298fc1c149afbf4c8996fb<wbr class="">92427ae41e4649b934ca495991b785<wbr class="">2b855]<br class="">
status: [1;"Unsupported protocol"]<br class="">
<br class="">
</div>
So I assume the HTTPS is not supported. Now if I understand correctly the alternative is to download the modules manually in $HOME/ExternalData and point to that folder through the variable ExternalData_OBJECT_STORES. The question is what do I need to download,
is that the only the two links above or there is more ? Is it maybe an option to change version of Cmake that can support that or/and how do I enable the support ?<br class="">
<br class="">
</div>
Any help is appreciated.<br class="">
</div>
Regards,<br class="">
</div>
Marco<span class=""> </span><br class="">
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C]<span class=""> </span><span dir="ltr" class=""><<a href="mailto:blowekamp@mail.nih.gov" target="_blank" class="">blowekamp@mail.nih.gov</a>></span>:<br class="">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Hello!<br class="">
<br class="">
OK, so it looks like you are using the current master branch of SimpleITK. I know this because you have the latest SimpleITK feature where CMake downloads the Superbuild dependencies with the CMake “ExternalData” module. This enables some interesting options
for your situation.<br class="">
<br class="">
You are on a cluster. On compute clusters, frequently the nodes don’t have access to the internet. So when cmake tries to download the URLS below it times out or errors. You can verify this with some command like “wget<span class=""> </span><a href="https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" rel="noreferrer" target="_blank" class="">https://midas3.kitware.<wbr class="">com/midas/api/rest?method=<wbr class="">midas.bitstream.download&<wbr class="">checksum=2e115fe26e435e33b0d5c<wbr class="">022e4490567&algorithm=MD5</a>”.
The alternative is that your version of CMake doesn’t support HTTPS. Yo can test this with the following script:<span class=""> </span><a href="https://github.com/conda-forge/cmake-feedstock/blob/master/recipe/SSLTest.cmake" rel="noreferrer" target="_blank" class="">https://github.com/<wbr class="">conda-forge/cmake-feedstock/<wbr class="">blob/master/recipe/SSLTest.<wbr class="">cmake</a><br class="">
<br class="">
Frequently, there are nodes on a cluster which have access to the internet for situations like this. You may be able to just use one of them.<br class="">
<br class="">
With the new ExternalData download module you may be able to pre-download these dependencies on the log in node. If you set the environment variable ExternalData_OBJECT_STORES to say “${HOME}/.ExternalData”, it will cache downloads to this directory. I assume
your home directory is available on the log in nodes. You can configure the SuperBuild there and build just the “SuperBuildSimpleITKSource” target. This will download the dependencies to the ExternaData directory. Then you can build in a cluster node, which
should use this cache.<br class="">
<br class="">
Also note when testing is enabled for the actual SimpleITK sub-project, a bunch of testing data is downloaded too. You can disable testing to avoid this, download and un-tar a Data archive [1], or replace the above procedure for this subproject.<br class="">
<br class="">
HTH,<br class="">
Brad<br class="">
<br class="">
[1]<span class=""> </span><a href="https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/Source/" rel="noreferrer" target="_blank" class="">https://sourceforge.net/<wbr class="">projects/simpleitk/files/<wbr class="">SimpleITK/0.10.0/Source/</a><br class="">
<div class="">
<div class=""><br class="">
<br class="">
> On Aug 17, 2016, at 10:26 AM, marco giordano <<a href="mailto:marco.giord@gmail.com" target="_blank" class="">marco.giord@gmail.com</a>> wrote:<br class="">
><br class="">
> Hi there,<br class="">
><br class="">
> I just downloaded SimpleTK and I tried to build it on a linux cluster (running Scientific Linux release 6.5- Carbon) using the superbuild.<br class="">
><br class="">
> I use cmake 3.3.1. The Generation of build files is fine, then when I try to build i get this:<br class="">
><br class="">
> -- Fetching "<a href="http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" rel="noreferrer" target="_blank" class="">http://midas3.kitware.com/mid<wbr class="">as/api/rest?method=midas.bitst<wbr class="">ream.download&checksum=2e115fe<wbr class="">26e435e33b0d5c022e4490567&algo<wbr class="">rithm=MD5</a>"<br class="">
> -- [download 100% complete]<br class="">
> -- Fetching "<a href="https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" rel="noreferrer" target="_blank" class="">https://midas3.kitware.com/mi<wbr class="">das/api/rest?method=midas.bits<wbr class="">tream.download&checksum=2e115f<wbr class="">e26e435e33b0d5c022e4490567&alg<wbr class="">orithm=MD5</a>"<br class="">
> -- Fetching "<a href="https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567" rel="noreferrer" target="_blank" class="">https://itk.org/files/Externa<wbr class="">lData/MD5/2e115fe26e435e33b0d5<wbr class="">c022e4490567</a>"<br class="">
> CMake Error at /cm/shared/apps/cmake/3.3.1/in<wbr class="">stall/share/cmake-3.3/Modules/<wbr class="">ExternalData.cmake:1012 (message):<br class="">
> Object MD5=2e115fe26e435e33b0d5c022e4<wbr class="">490567 not found at:<br class="">
><br class="">
> <a href="http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" rel="noreferrer" target="_blank" class="">http://midas3.kitware.com/mid<wbr class="">as/api/rest?method=midas.bitst<wbr class="">ream.download&checksum=2e115fe<wbr class="">26e435e33b0d5c022e4490567&algo<wbr class="">rithm=MD5</a><span class=""> </span>("Unsupported
protocol")<br class="">
> <a href="https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" rel="noreferrer" target="_blank" class="">https://midas3.kitware.com/mi<wbr class="">das/api/rest?method=midas.bits<wbr class="">tream.download&checksum=2e115f<wbr class="">e26e435e33b0d5c022e4490567&alg<wbr class="">orithm=MD5</a><span class=""> </span>("Unsupported
protocol")<br class="">
> <a href="https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567" rel="noreferrer" target="_blank" class="">https://itk.org/files/Externa<wbr class="">lData/MD5/2e115fe26e435e33b0d5<wbr class="">c022e4490567</a><span class=""> </span>("Unsupported
protocol")<br class="">
> Call Stack (most recent call first):<br class="">
> /cm/shared/apps/cmake/3.3.1/i<wbr class="">nstall/share/cmake-3.3/Modules<wbr class="">/ExternalData.cmake:1034 (_ExternalData_download_object<wbr class="">)<br class="">
><br class="">
><br class="">
> make[2]: *** [ExternalData/.ExternalSource/<wbr class="">lua-5.1.5.tar.gz.md5-stamp] Error 1<br class="">
> make[1]: *** [CMakeFiles/SuperBuildSimpleIT<wbr class="">KSourceReal.dir/all] Error 2<br class="">
><br class="">
> Any help is welcome.<br class="">
> Regards<br class="">
> --<br class="">
> Marco<br class="">
</div>
</div>
<div class="">
<div class="">> ______________________________<wbr class="">_______<br class="">
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<br clear="all" class="">
<br class="">
--<span class=""> </span><br class="">
<div data-smartmail="gmail_signature" class="">Marco Giordano<br class="">
<a href="SKYPE:marcogiord81" class="">SKYPE:marcogiord81</a></div>
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<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" class="">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important" class="">Please keep messages
on-topic and check the ITK FAQ at:</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" class="">
<a href="http://www.itk.org/Wiki/ITK_FAQ" style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank" class="">http://www.itk.org/Wiki/ITK_<wbr class="">FAQ</a><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" class="">
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<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important" class="">Follow this link
to subscribe/unsubscribe:</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" class="">
<a href="http://public.kitware.com/mailman/listinfo/insight-users" style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank" class="">http://public.kitware.com/<wbr class="">mailman/listinfo/insight-users</a></div>
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______________________________<wbr class="">_______<br class="">
Powered by <a href="http://www.kitware.com/" rel="noreferrer" target="_blank" class="">
www.kitware.com</a><br class="">
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Visit other Kitware open-source projects at<br class="">
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<br class="">
Kitware offers ITK Training Courses, for more information visit:<br class="">
<a href="http://www.kitware.com/products/protraining.php" rel="noreferrer" target="_blank" class="">http://www.kitware.com/<wbr class="">products/protraining.php</a><br class="">
<br class="">
Please keep messages on-topic and check the ITK FAQ at:<br class="">
<a href="http://www.itk.org/Wiki/ITK_FAQ" rel="noreferrer" target="_blank" class="">http://www.itk.org/Wiki/ITK_<wbr class="">FAQ</a><br class="">
<br class="">
Follow this link to subscribe/unsubscribe:<br class="">
<a href="http://public.kitware.com/mailman/listinfo/insight-users" rel="noreferrer" target="_blank" class="">http://public.kitware.com/<wbr class="">mailman/listinfo/insight-users</a><br class="">
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-- <br class="">
<div class="gmail_signature" data-smartmail="gmail_signature">Marco Giordano<br class="">
<a href="SKYPE:marcogiord81" class="">SKYPE:marcogiord81</a></div>
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