[ITK] [ITK-users] Error when Building SimpleITK with SuperBuild

Wed Aug 17 10:51:52 EDT 2016

Hello!

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.

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 https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5”. The alternative is that your version of CMake doesn’t support HTTPS. Yo can test this with the following script: https://github.com/conda-forge/cmake-feedstock/blob/master/recipe/SSLTest.cmake

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.

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.

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.

HTH,
Brad

[1] https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/Source/

> On Aug 17, 2016, at 10:26 AM, marco giordano <marco.giord at gmail.com> wrote:
> 
> Hi there,
> 
> I just downloaded SimpleTK and I tried to build it on a linux cluster (running Scientific Linux release 6.5- Carbon) using the superbuild. 
> 
> I use cmake 3.3.1. The Generation of build files is fine, then when I try to build i get this:
> 
> -- Fetching "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5"
> -- [download 100% complete]
> -- Fetching "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5"
> -- Fetching "https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567"
> CMake Error at /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message):
>   Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at:
> 
>     http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol")
>     https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol")
>     https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol")
> Call Stack (most recent call first):
>   /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 (_ExternalData_download_object)
> 
> 
> make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] Error 1
> make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2
> 
> Any help is welcome.
> Regards
> -- 
> Marco 
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