Comments (13)
AndresOrtegaGuerrero
commented on August 17, 2024
1
I tried this and then try to install the plugin with the app and it didnt work
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AndresOrtegaGuerrero
commented on August 17, 2024
1
I tested as you recommended before, indeed worked
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unkcpz
commented on August 17, 2024
1
Cool! Let's meet in person after your group meeting @mikibonacci ? We can decide where to add it.
I finally clean my laptop to run docker, so able to test together.
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mikibonacci
commented on August 17, 2024
I was able to install (a posteriori) h5py in this way:
conda install hdf5
HDF5_DIR=/opt/conda/ pip install h5pyHDF5 version: hdf5 1.14.0 nompi_h96fea9c_103 conda-forge
h5py version: 3.11.0
Maybe we can install hdf5 (via conda) and define HDF5_DIR when we build the docker. Hopefully it will not affect much the performances? @unkcpz, do you have comments?
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unkcpz
commented on August 17, 2024
Okay, let's add it to full-stack.
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mikibonacci
commented on August 17, 2024
I Will try again and see if I encounter the issue. I will keep you updated on this
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unkcpz
commented on August 17, 2024
Can you install h5py with apt??
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unkcpz
commented on August 17, 2024
Okay, let's add it to full-stack.
Or if it is QE specific, we just add it here would be better. Let me know if install this really solve the problem. I'll add it to the image.
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AndresOrtegaGuerrero
commented on August 17, 2024
I tried @mikibonacci solution and it works for me , so I guess we need to modified the image or the plugin?
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mikibonacci
commented on August 17, 2024
I think we should add in the dockerfile (as conda installation and ENV var definition probably is easy), but I am not sure where to put the commands. @unkcpz I'll let you decide as you know for sure the best place. (if you can also explain to me in person, very much appreciated :) )
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mikibonacci
commented on August 17, 2024
It is possible to install h5py via apt, as explained here, but I am not sure is better approach than the one I followed.
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mikibonacci
commented on August 17, 2024
So, I tried to install h5py via conda, and it worked: conda installl h5py=3.11.0 ; this automatically deals with hdf5 installation. @AndresOrtegaGuerrero and @unkcpz, do you mind test this method? for me it worked as expected and then I was able to install the vibro plugin.
Several packages are installed/updated (15.6 MB):
(base) jovyan@4d4dd4a921a9:~$ conda install h5py=3.11.0
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 22.9.0
latest version: 24.5.0
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /opt/conda
added / updated specs:
- h5py=3.11.0
The following packages will be downloaded:
package | build
---------------------------|-----------------
c-ares-1.28.1 | h31becfc_0 172 KB conda-forge
ca-certificates-2024.6.2 | hcefe29a_0 152 KB conda-forge
cached-property-1.5.2 | hd8ed1ab_1 4 KB conda-forge
cached_property-1.5.2 | pyha770c72_1 11 KB conda-forge
certifi-2024.2.2 | pyhd8ed1ab_0 157 KB conda-forge
h5py-3.11.0 |nompi_py39h07eddff_101 1.1 MB conda-forge
hdf5-1.14.3 |nompi_hd1676c9_103 3.8 MB conda-forge
krb5-1.21.2 | hc419048_0 1.4 MB conda-forge
libaec-1.1.3 | h2f0025b_0 35 KB conda-forge
libcurl-8.8.0 | h4e8248e_0 407 KB conda-forge
libgfortran-ng-13.2.0 | he9431aa_0 23 KB conda-forge
libgfortran5-13.2.0 | h582850c_0 1.0 MB conda-forge
libnghttp2-1.58.0 | hb0e430d_1 662 KB conda-forge
libpq-16.3 | hcf0348d_0 2.4 MB conda-forge
libssh2-1.11.0 | h492db2e_0 278 KB conda-forge
openssl-3.3.0 | h68df207_3 3.3 MB conda-forge
psycopg2-2.9.9 | py39h77becb1_0 171 KB conda-forge
psycopg2-binary-2.9.9 | pyhd8ed1ab_0 10 KB conda-forge
zstd-1.5.6 | h02f22dd_0 527 KB conda-forge
------------------------------------------------------------
Total: 15.6 MB
The following NEW packages will be INSTALLED:
cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1 None
cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1 None
h5py conda-forge/linux-aarch64::h5py-3.11.0-nompi_py39h07eddff_101 None
hdf5 conda-forge/linux-aarch64::hdf5-1.14.3-nompi_hd1676c9_103 None
libaec conda-forge/linux-aarch64::libaec-1.1.3-h2f0025b_0 None
The following packages will be UPDATED:
c-ares 1.18.1-hf897c2e_0 --> 1.28.1-h31becfc_0 None
ca-certificates 2023.5.7-hcefe29a_0 --> 2024.6.2-hcefe29a_0 None
certifi 2023.5.7-pyhd8ed1ab_0 --> 2024.2.2-pyhd8ed1ab_0 None
krb5 1.20.1-h113d92e_0 --> 1.21.2-hc419048_0 None
libcurl 8.1.1-hc34909b_0 --> 8.8.0-h4e8248e_0 None
libgfortran-ng 12.2.0-he9431aa_19 --> 13.2.0-he9431aa_0 None
libgfortran5 12.2.0-hf695500_19 --> 13.2.0-h582850c_0 None
libnghttp2 1.52.0-h250e5c5_0 --> 1.58.0-hb0e430d_1 None
libpq 15.3-hf616e62_1 --> 16.3-hcf0348d_0 None
libssh2 1.10.0-he5a64b1_3 --> 1.11.0-h492db2e_0 None
openssl 3.1.0-h31becfc_3 --> 3.3.0-h68df207_3 None
psycopg2 2.9.3-py39ha828215_2 --> 2.9.9-py39h77becb1_0 None
psycopg2-binary 2.9.3-pyhd8ed1ab_2 --> 2.9.9-pyhd8ed1ab_0 None
zstd 1.5.2-hc1e27d5_4 --> 1.5.6-h02f22dd_0 Nonefrom aiidalab-qe.
mikibonacci
commented on August 17, 2024
solved with aiidalab/aiidalab-docker-stack#468
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Related Issues (20)
- Improve code setup HOT 1
- Job List not displaying, Checkbox instance expected a unicode string, not the float nan HOT 3
- Issue in optimade provider selection
- Exclude all other plugins when select the HP plugin
- Include Bands projections
- Handling Molecules HOT 3
- Docker image for fast launch
- Time report for each sub WorkChain HOT 1
- Time estimation to run a given simulation HOT 1
- Automatic parallelization settings
- Adding more QE codes into the default stored ones HOT 1
- Plugin list should install external as pip install --user
- App crashes if dos.x code is not on the same computer of pw.x
- Adding an upload button to setup computer and codes
- nsteps widget
- Acknowledgements for projects
- Rename `QuantumESPRESSO` to `Quantum ESPRESSO`
- Walltime doesnt apply to plugin (vibroscopy) HOT 1
- Case sensitive filenames breaks in case insensitive filesystems. HOT 1
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