[ITK-users] Error when Building SimpleITK with SuperBuild

Thu Aug 18 08:53:48 EDT 2016

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/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: [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 $HOME/ExternalData and
>> point to that folder through the variable ExternalData_OBJECT_STORES. The
>> question is what do I need to download, is that the only the two links
>> above or there is more ? Is it maybe an option to change version of Cmake
>> that can support that or/and how do I enable the support ?
>>
>> Any help is appreciated.
>> Regards,
>> Marco
>>
>> 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] <
>> blowekamp at mail.nih.gov>:
>>
>>> Hello!
>>>
>>> OK, so it looks like you are using the current master branch of
>>> SimpleITK. I know this because you have the latest SimpleITK feature where
>>> CMake downloads the Superbuild dependencies with the CMake “ExternalData”
>>> module. This enables some interesting options for your situation.
>>>
>>> You are on a cluster. On compute clusters, frequently the nodes don’t
>>> have access to the internet. So when cmake tries to download the URLS below
>>> it times out or errors. You can verify this with some command like “wget
>>> https://midas3.kitware.com/midas/api/rest?method=midas.bitst
>>> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5”.
>>> The alternative is that your version of CMake doesn’t support HTTPS. Yo can
>>> test this with the following script: https://github.com/conda-forge
>>> /cmake-feedstock/blob/master/recipe/SSLTest.cmake
>>>
>>> Frequently, there are nodes on a cluster which have access to the
>>> internet for situations like this. You may be able to just use one of them.
>>>
>>> With the new ExternalData download module you may be able to
>>> pre-download these dependencies on the log in node. If you set the
>>> environment variable ExternalData_OBJECT_STORES to say
>>> “${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
>>> > _____________________________________
>>> > 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
>>>
>>>
>>
>>
>> --
>> 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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20160818/49eb8d6c/attachment.html>