[ITK-users] Error when Building SimpleITK with SuperBuild

Thu Aug 18 09:28:41 EDT 2016

And for the lazier there are now CMake binaries for Linux i386 and x86_64.

https://cmake.org/download/

On Aug 18, 2016, at 8:53 AM, Dženan Zukić <dzenanz at gmail.com> wrote:

Hi Marco,

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.

Regards,
Dženan

On Thu, Aug 18, 2016 at 6:14 AM, Richard Beare <richard.beare at gmail.com<mailto:richard.beare at gmail.com>> wrote:
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<mailto: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/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<mailto: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<mailto: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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Kitware offers ITK Training Courses, for more information visit:
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