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Installation challenges #196
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Thanks, this is very important information. The recommended way to install simex is using cmake. install.sh serves as a guideline. More hints may be found in .travis.yml and in scripts under Installation has successfully been tested on various linux distributions including debian7+ ubuntu 14.04+, centos7. What is your target? c compiler? hdf version? cmake version? mpi ? mkl? where does it fail if you enable more components? which ones? |
Thanks Carsten! In the first instance I want to install it on Maxwell (I know there's already a module, but I want to test a branch @ejcjason is working on). So CentOS 7. I'll focus on the conda installation for now. Once I've got a direct installation working, I might take an interest in using Spack to install it, and/or containerising it. So, I've recreated a conda environment using This time it worked. Previously I tried for longer with other modules enabled, and something I installed for one of the other modules seemed to break WPG. I'll experiment further and get back to you. |
This is a bit long, but I figure it's worth recording the details of what errors I'm getting and what I'm trying. I should also have mentioned that I turned Disable WPG (for now), enable CrystFEL.
I didn't see this one before. I recall there was a change in the way conda works at some point, and now the recommendation is to install a compiler from conda, so you're not using something outside the environment. Maybe I'm running into some symptom of that.
Now we're using a compiler in conda, it no longer uses libraries from the system, if I've understood correctly. This is the first of a series of problems building CrystFEL which I ran into before, so let's install several packages I already found it needs: Building CrystFEL now works. Re-enable WPG.
Missing a C++ compiler? Trying
This is where I got stuck last time around. Summary: Relying on compilers & libraries on the system, I can build WPG, but building CrystFEL fails. By installing compilers in the conda environment, I can get CrystFEL to build, but then WPG fails, and I've not yet worked out how to solve that. |
since you try this on maxwell, there is a functional installation on
maxwell under /data/netapp/s2e/simex
$> module load intel/2018
$> module load mpi/openmpi-x86_64-intel
annoyingly, you have to clean up your PYTHONPATH after this (remove the
py2.7 part of it).
then:
$> source /data/netapp/s2e/simex/bin/simex_vars.sh
test:
$> python
>> from SimEx import *
Hope this helps.
…--
Dr. Carsten Fortmann-Grote
PaNOSC WP5 leader
On 5/6/20 10:49 AM, Thomas Kluyver wrote:
This is a bit long, but I figure it's worth recording the details of
what errors I'm getting and what I'm trying. I should also have
mentioned that I turned |DEVELOPER_MODE| off on @ejcjason
<https://github.com/ejcjason>'s suggestion.
Disable WPG (for now), enable CrystFEL.
|/home/kluyvert/.conda/envs/simex/lib/libpng16.so.16: undefined
reference to ***@***.***_1.2.9' |
I didn't see this one before. |conda install zlib| ? No, that doesn't
fix it. |conda install libpng| ? Replaces a |conda-forge| package with
one from the default channel. No, still the same error.
I recall there was a change in the way conda works
<https://www.anaconda.com/blog/utilizing-the-new-compilers-in-anaconda-distribution-5>
at some point, and now the recommendation is to install a compiler from
conda, so you're not using something outside the environment. Maybe I'm
running into some symptom of that. |conda install gcc_linux-64| .
|src/utils.h:41:10: fatal error: gsl/gsl_matrix.h: No such file or
directory |
Now we're using a compiler in conda, it no longer uses libraries from
the system, if I've understood correctly. This is the first of a series
of problems building CrystFEL which I ran into before, so let's install
several packages I already found it needs: |conda install gsl cairo
pango gdk-pixbuf| .
Building CrystFEL now works. Re-enable WPG.
|x86_64-conda_cos6-linux-gnu-cc: error trying to exec 'cc1plus': execvp:
No such file or directory |
Missing a C++ compiler? Trying |conda install gxx_linux-64| .
|/home/kluyvert/.conda/envs/simex/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
cannot find -lgomp |
This is where I got stuck last time around. |conda install libgomp| . A
package gets installed, but I still get the same error. This appears to
come while building |srwlpy| for |XFELPhotonPropagator|.
*Summary:* Relying on compilers & libraries on the system, I can build
WPG, but building CrystFEL fails. By installing compilers in the conda
environment, I can get CrystFEL to build, but then WPG fails, and I've
not yet worked out how to solve that.
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|
hi thomas,
you need intel omp: module load intel
…--
Dr. Carsten Fortmann-Grote
PaNOSC WP5 leader
On 5/6/20 10:49 AM, Thomas Kluyver wrote:
This is a bit long, but I figure it's worth recording the details of
what errors I'm getting and what I'm trying. I should also have
mentioned that I turned |DEVELOPER_MODE| off on @ejcjason
<https://github.com/ejcjason>'s suggestion.
Disable WPG (for now), enable CrystFEL.
|/home/kluyvert/.conda/envs/simex/lib/libpng16.so.16: undefined
reference to ***@***.***_1.2.9' |
I didn't see this one before. |conda install zlib| ? No, that doesn't
fix it. |conda install libpng| ? Replaces a |conda-forge| package with
one from the default channel. No, still the same error.
I recall there was a change in the way conda works
<https://www.anaconda.com/blog/utilizing-the-new-compilers-in-anaconda-distribution-5>
at some point, and now the recommendation is to install a compiler from
conda, so you're not using something outside the environment. Maybe I'm
running into some symptom of that. |conda install gcc_linux-64| .
|src/utils.h:41:10: fatal error: gsl/gsl_matrix.h: No such file or
directory |
Now we're using a compiler in conda, it no longer uses libraries from
the system, if I've understood correctly. This is the first of a series
of problems building CrystFEL which I ran into before, so let's install
several packages I already found it needs: |conda install gsl cairo
pango gdk-pixbuf| .
Building CrystFEL now works. Re-enable WPG.
|x86_64-conda_cos6-linux-gnu-cc: error trying to exec 'cc1plus': execvp:
No such file or directory |
Missing a C++ compiler? Trying |conda install gxx_linux-64| .
|/home/kluyvert/.conda/envs/simex/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
cannot find -lgomp |
This is where I got stuck last time around. |conda install libgomp| . A
package gets installed, but I still get the same error. This appears to
come while building |srwlpy| for |XFELPhotonPropagator|.
*Summary:* Relying on compilers & libraries on the system, I can build
WPG, but building CrystFEL fails. By installing compilers in the conda
environment, I can get CrystFEL to build, but then WPG fails, and I've
not yet worked out how to solve that.
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@CFGrote I can talk to Frank, we don't support Python 2.7 any more, so maybe it makes sense to modify the module to not set the python path... |
Thanks Carsten. I found the module, but I was trying to test a branch that @ejcjason was working on, so I want to do the installation myself. I'll try building it with the |
I tried with |
have you run
```
$> source `which compilervars.sh` intel64
```
assuming you are on a 64bit machine. that loads the intel lib and
include paths.
carsten
…--
Dr. Carsten Fortmann-Grote
PaNOSC WP5 leader
On 5/15/20 5:06 PM, Thomas Kluyver wrote:
I tried with |module load intel| (it seems to have picked |intel/2020|
as the default version), but I still see the same error about |-lgomp|.
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What's the recommended way to install SimEx? I've been looking at various things without much success:
install.sh
and commenting out various imports in the Python code, but this doesn't feel like a good answer..deb
package, but it's from a few years ago, and my target isn't Debian-based anyway.Docker/simex
within the repository, but it fell down pretty quickly. I haven't investigated this much, but I see the docker folder hasn't been touched for 2 years, so I doubt you're using that frequently.The text was updated successfully, but these errors were encountered: