[ITK] [ITK-users] Error when Building SimpleITK with SuperBuild
Lowekamp, Bradley (NIH/NLM/LHC) [C]
blowekamp at mail.nih.gov
Thu Aug 18 12:13:56 EDT 2016
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<mailto: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<mailto: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<mailto: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
> _____________________________________
> Powered by www.kitware.com<http://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<http://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<http://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<http://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<http://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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/community/attachments/20160818/a4039443/attachment-0001.html>
-------------- next part --------------
_____________________________________
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
More information about the Community
mailing list