[ITK-users] Error when Building SimpleITK with SuperBuild

Thu Aug 18 12:04:47 EDT 2016

Thanks a lot for the help,
I downloaded the Cmake binary and now it seems it is able to download,
however the build process gets stuck at cloning ITK:

-- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua
[ 18%] Completed 'Lua'
[ 18%] Built target Lua
[ 20%] Creating directories for 'ITK'
[ 21%] Performing download step (git clone) for 'ITK'
Cloning into 'ITK'...
Install the project...
-- Install configuration: "Release"
-- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua
[ 18%] Completed 'Lua'
[ 18%] Built target Lua
[ 20%] Creating directories for 'ITK'
[ 21%] Performing download step (git clone) for 'ITK'
Cloning into 'ITK'...

Maybe a wrong link somewhere ?
Regards

2016-08-18 15:28 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov>:

> 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>
> 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>
>> 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=2e115fe26e435e33b0d5c
>>> 022e4490567&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: [f8c925402b90f74566f71e64eea7b
>>> b9d83daac69cde71408ffd6c043be6a4991]
>>>         actual hash: [e3b0c44298fc1c149afbf4c8996fb
>>> 92427ae41e4649b934ca495991b7852b855]
>>>              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 $HOME/ExternalData
>>> and point to that folder through the variable ExternalData_OBJECT_STORES.
>>> The question is what do I need to download, is that the only the two links
>>> above or there is more ? Is it maybe an option to change version of Cmake
>>> that can support that or/and how do I enable the support ?
>>>
>>> Any help is appreciated.
>>> Regards,
>>> Marco
>>>
>>> 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] <
>>> blowekamp at mail.nih.gov>:
>>>
>>>> Hello!
>>>>
>>>> OK, so it looks like you are using the current master branch of
>>>> SimpleITK. I know this because you have the latest SimpleITK feature where
>>>> CMake downloads the Superbuild dependencies with the CMake “ExternalData”
>>>> module. This enables some interesting options for your situation.
>>>>
>>>> You are on a cluster. On compute clusters, frequently the nodes don’t
>>>> have access to the internet. So when cmake tries to download the URLS below
>>>> it times out or errors. You can verify this with some command like “wget
>>>>  https://midas3.kitware.com/midas/api/rest?method=
>>>> midas.bitstream.download&checksum=2e115fe26e435e33b0d5c
>>>> 022e4490567&algorithm=MD5”. The alternative is that your version of
>>>> CMake doesn’t support HTTPS. Yo can test this with the following script:
>>>>  https://github.com/conda-forge/cmake-feedstock/
>>>> blob/master/recipe/SSLTest.cmake
>>>>
>>>> Frequently, there are nodes on a cluster which have access to the
>>>> internet for situations like this. You may be able to just use one of them.
>>>>
>>>> With the new ExternalData download module you may be able to
>>>> pre-download these dependencies on the log in node. If you set the
>>>> environment variable ExternalData_OBJECT_STORES to say
>>>> “${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
>>>> > _____________________________________
>>>> > Powered by www.kitware.com
>>>> >
>>>> > Visit other Kitware open-source projects at
>>>> > http://www.kitware.com/opensource/opensource.html
>>>> >
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>>>> > http://www.kitware.com/products/protraining.php
>>>> >
>>>> > Please keep messages on-topic and check the ITK FAQ at:
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>>>>
>>>>
>>>
>>>
>>> --
>>> Marco Giordano
>>> SKYPE:marcogiord81
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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>

-- 
Marco Giordano
SKYPE:marcogiord81
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