[ITK-users] Error when Building SimpleITK with SuperBuild

Mon Aug 22 04:53:04 EDT 2016

Finally I managed to build SimpleITK on the cluster node. Despite the
suggestions I could not manage to clone ITK through the build process
(still not sure why, maybe the git version 1.7.7.3?) but I could clone it
separately and then set the ITK_REPOSITORY variable to the repository and
it worked. Thanks a lot.
regards

2016-08-18 18:13 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov>:

> Hi!
>
> The lack of error message is not helpful to assist with debugging. You
> must try to reproduce the problem on the node then.
>
> Try running “git clone https://itk.org/ITK.git” and see if it produces
> more output.
>
> The probable problems are there is network restrictions on your cluster
> node, or that your git version is too old and does not support the https
> protocol.
>
> You could try changing the CMake variable SITK_GIT_PROTOCOL from “https”
> to “git” [1]. Currently there is not “ExternalData” cache work around for
> this.
>
> HTH,
> Brad
>
> [1] https://github.com/SimpleITK/SimpleITK/blob/master/
> SuperBuild/External_ITK.cmake#L36
>
> On Aug 18, 2016, at 12:04 PM, marco giordano <marco.giord at gmail.com>
> wrote:
>
> 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=
>>>> 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: [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 $HOME/ExternalData
>>>> and point to that folder through the variable ExternalData_OBJECT_STORES.
>>>> The question is what do I need to download, is that the only the two links
>>>> above or there is more ? Is it maybe an option to change version of Cmake
>>>> that can support that or/and how do I enable the support ?
>>>>
>>>> Any help is appreciated.
>>>> Regards,
>>>> Marco
>>>>
>>>> 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] <
>>>> blowekamp at mail.nih.gov>:
>>>>
>>>>> Hello!
>>>>>
>>>>> OK, so it looks like you are using the current master branch of
>>>>> SimpleITK. I know this because you have the latest SimpleITK feature where
>>>>> CMake downloads the Superbuild dependencies with the CMake “ExternalData”
>>>>> module. This enables some interesting options for your situation.
>>>>>
>>>>> You are on a cluster. On compute clusters, frequently the nodes don’t
>>>>> have access to the internet. So when cmake tries to download the URLS below
>>>>> it times out or errors. You can verify this with some command like “wget
>>>>>  https://midas3.kitware.com/midas/api/rest?method=midas
>>>>> .bitstream.download&checksum=2e115fe26e435e33b0d5c022e44905
>>>>> 67&algorithm=MD5”. The alternative is that your version of CMake
>>>>> doesn’t support HTTPS. Yo can test this with the following script:
>>>>> https://github.com/conda-forge/cmake-feedstock/blob/
>>>>> master/recipe/SSLTest.cmake
>>>>>
>>>>> Frequently, there are nodes on a cluster which have access to the
>>>>> internet for situations like this. You may be able to just use one of them.
>>>>>
>>>>> With the new ExternalData download module you may be able to
>>>>> pre-download these dependencies on the log in node. If you set the
>>>>> environment variable ExternalData_OBJECT_STORES to say
>>>>> “${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/SimpleI
>>>>> TK/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
>>>>> >
>>>>> > 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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>>>>> >
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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
>>>>
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>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
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>>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
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>>>
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>>> http://www.kitware.com/products/protraining.php
>>>
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>> _____________________________________
>> 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
>>
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>> 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
>>
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>>
>
>
> --
> Marco Giordano
> SKYPE:marcogiord81
>
>
>

-- 
Marco Giordano
SKYPE:marcogiord81
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