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

marco giordano marco.giord at gmail.com
Thu Aug 18 05:37:57 EDT 2016 

Hi there,
I checked the internet connection on the node and seems fine (I can
download with wget the https://midas3.kitware.com/
midas/api/rest?method=midas.bitstream.download&checksum=
2e115fe26e435e33b0d5c022e4490567&algorithm=MD5”).

I run the script SSLTest.cmake
<https://github.com/conda-forge/cmake-feedstock/blob/master/recipe/SSLTest.cmake>
but it fails (it downloads a LICENSE file but it is empty):
CMake Error at SSLTest.cmake:5 (file):
  file DOWNLOAD HASH mismatch

    for file: [/home/mgiordano/code/SimpleITK/LICENSE]
      expected hash:
[f8c925402b90f74566f71e64eea7bb9d83daac69cde71408ffd6c043be6a4991]
        actual hash:
[e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855]
             status: [1;"Unsupported protocol"]

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 ?

Any help is appreciated.
Regards,
Marco

2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov>:

> 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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>


-- 
Marco Giordano
SKYPE:marcogiord81
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