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

Richard Beare richard.beare at gmail.com
Thu Aug 18 06:14:43 EDT 2016 

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.

On Thu, Aug 18, 2016 at 7:37 PM, marco giordano <marco.giord at gmail.com>
wrote:

> Hi there,
> I checked the internet connection on the node and seems fine (I can
> download with wget the https://midas3.kitware.com/mid
> as/api/rest?method=midas.bitstream.download&checksum=2e115fe
> 26e435e33b0d5c022e4490567&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: [f8c925402b90f74566f71e64eea7bb
> 9d83daac69cde71408ffd6c043be6a4991]
>         actual hash: [e3b0c44298fc1c149afbf4c8996fb9
> 2427ae41e4649b934ca495991b7852b855]
>              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 $HOME/ExternalData and
> point to that folder through the variable ExternalData_OBJECT_STORES. The
> question is what do I need to download, is that the only the two links
> above or there is more ? Is it maybe an option to change version of Cmake
> that can support that or/and how do I enable the support ?
>
> Any help is appreciated.
> Regards,
> Marco
>
> 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] <
> blowekamp at mail.nih.gov>:
>
>> Hello!
>>
>> OK, so it looks like you are using the current master branch of
>> SimpleITK. I know this because you have the latest SimpleITK feature where
>> CMake downloads the Superbuild dependencies with the CMake “ExternalData”
>> module. This enables some interesting options for your situation.
>>
>> You are on a cluster. On compute clusters, frequently the nodes don’t
>> have access to the internet. So when cmake tries to download the URLS below
>> it times out or errors. You can verify this with some command like “wget
>> https://midas3.kitware.com/midas/api/rest?method=midas.bitst
>> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5”.
>> The alternative is that your version of CMake doesn’t support HTTPS. Yo can
>> test this with the following script: https://github.com/conda-forge
>> /cmake-feedstock/blob/master/recipe/SSLTest.cmake
>>
>> Frequently, there are nodes on a cluster which have access to the
>> internet for situations like this. You may be able to just use one of them.
>>
>> With the new ExternalData download module you may be able to pre-download
>> these dependencies on the log in node. If you set the environment variable
>> ExternalData_OBJECT_STORES to say “${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/mid
>> as/api/rest?method=midas.bitstream.download&checksum=2e115fe
>> 26e435e33b0d5c022e4490567&algorithm=MD5"
>> > -- [download 100% complete]
>> > -- Fetching "https://midas3.kitware.com/mi
>> das/api/rest?method=midas.bitstream.download&checksum=2e115f
>> e26e435e33b0d5c022e4490567&algorithm=MD5"
>> > -- Fetching "https://itk.org/files/Externa
>> lData/MD5/2e115fe26e435e33b0d5c022e4490567"
>> > CMake Error at /cm/shared/apps/cmake/3.3.1/in
>> stall/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message):
>> >   Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at:
>> >
>> >     http://midas3.kitware.com/midas/api/rest?method=midas.bitst
>> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5
>> ("Unsupported protocol")
>> >     https://midas3.kitware.com/midas/api/rest?method=midas.bits
>> tream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5
>> ("Unsupported protocol")
>> >     https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5
>> c022e4490567 ("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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>
> Visit other Kitware open-source projects at
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> Kitware offers ITK Training Courses, for more information visit:
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> Please keep messages on-topic and check the ITK FAQ at:
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