undefined reference to `memcpy@GLIBC_2.14'

[njhunsak]

Unfortunately I will not be able to use the Docker option on the computing cluster I have access to so I have to compile it myself. However, I continue to get the following issue (see attached image). The compute cluster runs Red Hat Enterprise Linux Server release 6.6 (Santiago), so different from running this on Ubuntu 14.04. I also tried to compile mindboggle on a local computer running Ubuntu 16.04 and I get the same error code. Thoughts? Naomi.

[binarybottle]

Dear Naomi,

Did you try to install this from the install_mindboggle.sh script? That script uses miniconda, which is supposed to make it easier to access dependencies such as VTK. It would be really easy for people to install a non-container version of Mindboggle with a conda-forge entry for mindboggle, but I don't know how to go about building that. Alternatively, if your cluster allows access to Singularity (http://singularity.lbl.gov/), all Docker containers can be transformed into Singularity images.

On Mon, Nov 7, 2016 at 2:07 PM, Naomi H. notifications@github.com wrote:

Unfortunately I will not be able to use the Docker option on the computing cluster I have access to so I have to compile it myself. However, I continue to get the following issue (see attached image). The compute cluster runs Red Hat Enterprise Linux Server release 6.6 (Santiago), so different from running this on Ubuntu 14.04. I also tried to compile mindboggle on a local computer running Ubuntu 16.04 and I get the same error code. Thoughts? Naomi. [image: screen shot 2016-11-03 at 12 08 11 pm] https://cloud.githubusercontent.com/assets/4333838/20071680/a2f8ce76-a4e2-11e6-8034-62ac18008118.png

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/nipy/mindboggle/issues/82, or mute the thread https://github.com/notifications/unsubscribe-auth/AAOb9GZ29DP7FcbNvF8k8IRIPOkrsRWlks5q73b8gaJpZM4Krl3B .

[njhunsak]

I am trying to install from the install_mindboggle.sh script and got the error even though I am using miniconda. I'll look into the singularity option as well. Thanks. Naomi

[binarybottle]

I'm sorry you are having difficulty. Please do tell me how your Singularity attempt goes!

On Mon, Nov 7, 2016 at 2:07 PM Naomi H. notifications@github.com wrote:

Unfortunately I will not be able to use the Docker option on the computing cluster I have access to so I have to compile it myself. However, I continue to get the following issue (see attached image). The compute cluster runs Red Hat Enterprise Linux Server release 6.6 (Santiago), so different from running this on Ubuntu 14.04. I also tried to compile mindboggle on a local computer running Ubuntu 16.04 and I get the same error code. Thoughts? Naomi. [image: screen shot 2016-11-03 at 12 08 11 pm] https://cloud.githubusercontent.com/assets/4333838/20071680/a2f8ce76-a4e2-11e6-8034-62ac18008118.png

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/nipy/mindboggle/issues/82, or mute the thread https://github.com/notifications/unsubscribe-auth/AAOb9GZ29DP7FcbNvF8k8IRIPOkrsRWlks5q73b8gaJpZM4Krl3B .

[njhunsak]

Singularity is a no go on my cluster, but it seems like I can't get mindboggle to run on any system I have access to using the install script or Docker. When I run the docker build -t bids/mindboggle .; command, it fails (here's the full output of that process: build.txt). Interestingly though, I'm able to run docker run --rm -ti -v $PATH_ON_HOST:/root/data --entrypoint /bin/bash bids/mindboggle with no problems. The Docker container starts; however it looks like ANTs isn't installed or available through the Docker (here's the full text output: volume_only.txt):

HOST=/root/data/Users/njhunsak;
FREESURFER_SUBJECT=$HOST/mindboggle_input_example/freesurfer/subjects/arno;
ANTS_SUBJECT=$HOST/mindboggle_input_example/ants/subjects/arno;
MINDBOGGLING=$HOST/mindboggling;
MINDBOGGLED=$HOST/mindboggled;
mindboggle $FREESURFER_SUBJECT --no_surfaces --cpus 8 --working $MINDBOGGLING --out $MINDBOGGLED --ants $ANTS_SUBJECT/antsBrainSegmentation.nii.gz
/usr/local/miniconda/lib/python3.5/site-packages/scipy/ndimage/interpolation.py:430: UserWarning: The behaviour of affine_transform with a one-dimensional array supplied for the matrix parameter has changed in scipy 0.18.0.
  "The behaviour of affine_transform with a one-dimensional "
sh: ThresholdImage: command not found
sh: ImageMath: command not found
sh: ThresholdImage: command not found
sh: ImageMath: command not found
Traceback (most recent call last):
  File "/usr/local/miniconda/bin/mindboggle", line 2447, in <module>
    mbFlow.run(plugin=args.plugin)
  File "/usr/local/miniconda/lib/python3.5/site-packages/nipype/pipeline/engine/workflows.py", line 597, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/usr/local/miniconda/lib/python3.5/site-packages/nipype/pipeline/plugins/linear.py", line 57, in run
    report_nodes_not_run(notrun)
  File "/usr/local/miniconda/lib/python3.5/site-packages/nipype/pipeline/plugins/base.py", line 95, in report_nodes_not_run
    raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details

I really really want this pipeline to run and have been waiting for it for years!! Thanks for your patience: Naomi

[njhunsak]

I was able to get docker to build once I made these edits to the Dockerfile:

# Enable neurodebian
# RUN curl -sSL http://neuro.debian.net/lists/vivid.de-m.full | tee /etc/apt/sources.list.d/neurodebian.sources.list && \
#     curl -sSL http://neuro.debian.net/lists/vivid.us-tn.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
#     apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9 && \
#     apt-get update #&& \

RUN curl -sSL http://neuro.debian.net/lists/vivid.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list && \
    apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9 && \
    apt-get update #&& \

After I ran docker build -t bids/mindboggle .; successfully, I was able to run docker run --rm -ti -v $PATH_ON_HOST:/root/data --entrypoint /bin/bash bids/mindboggle;. Right now I'm using the "mindboggle_input_example" data set to see if it runs and so far so good.

Naomi

[binarybottle]

This is great news! Thank you for helping to find a fix to the build!

[binarybottle]

@akeshavan fixed the Dockerfile after you pointed out the change that needed to be made, and the new one on github (https://github.com/BIDS-Apps/mindboggle/blob/master/Dockerfile) has been working for me. Shall I close this issue?

[binarybottle]

@njhunsak -- As logged in https://github.com/nipy/mindboggle/issues/83, I just tested out both the Docker and non-Docker (in a Virtualbox Ubuntu 14.04 virtual machine) installations on my MacOS laptop, and Mindboggle ran to completion for both setups. I am closing this issue, but please feel free to reopen it if you run into trouble. Thank you again for your help!