Difference between revisions of "UCVM Install"
From SCECpedia
Jump to navigationJump to search| Line 9: | Line 9: | ||
6) When it prompts to update .bashrc (or .bash_profile) say yes | 6) When it prompts to update .bashrc (or .bash_profile) say yes | ||
| − | 7) Confirm .bashrc | + | 7) Confirm .bashrc contains |
# >>> conda initialize >>> | # >>> conda initialize >>> | ||
# !! Contents within this block are managed by 'conda init' !! | # !! Contents within this block are managed by 'conda init' !! | ||
| Line 78: | Line 78: | ||
env | grep UCVM | env | grep UCVM | ||
| − | |||
| + | 16) move to /home1/<username>/test_ucvm | ||
| + | list the installed modules | ||
| + | ucvm_query -H | ||
| − | + | ucvm_query with a list of lon-lat-depth in a file | |
| − | ucvm_query - | + | |
| − | ucvm_query -f /project/username/ucvm_bin/conf/ucvm.conf -m cvmsi | + | ucvm_query -f /project/username/ucvm_bin/conf/ucvm.conf -m cvmsi < /project/username/ucvm_bin/tests/inputs/test_latlons.txt |
| − | </ | ||
== Terminal Message to User - Successful Installation Completes == | == Terminal Message to User - Successful Installation Completes == | ||
Revision as of 07:15, 30 March 2021
Contents
Installation on discovery.usc.edu
0) confirm login and home directory /home1/<username>
1) create test_ucvm subdirectory for use later
3) confirm /project/scec_608/<username> exists
4) copy Anaconda Linux install script from /project/maechlin_162
5) run script and give installation directory as
/project/scec_608/<username>/anaconda3 as install path
6) When it prompts to update .bashrc (or .bash_profile) say yes
7) Confirm .bashrc contains
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/project/scec_608/<username>/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/project/scec_608/<username>/anaconda3/etc/profile.d/conda.sh" ]; then
. "/project/scec_608/<username>/anaconda3/etc/profile.d/conda.sh"
else
export PATH="/project/scec_608/<username>/anaconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
8) add module unload/load command into .bash_profile
module purge
module load gcc/8.3.0
module load openmpi/4.0.2
module load pmix/3.1.3
# Setup UCVM Environment
export LD_PRELOAD=/spack/apps/gcc/8.3.0/lib64/libstdc++.so.6
source /project/scec_608/<username>/ucvm_bin/conf/ucvm_env.sh
9) log out and log back in
10) confirm anaconda python is picked up
which python
11) create /project/scec_608/<username>/ucvm directory
12) cd into directory and type
git clone --branch toPython3 https://github.com/SCECcode/UCVMC.git
13) cd into /project/scec_608/<username>/ucvm_src/
Currently, we stage the largefiles externally, giving the user options on how they
assemble the list of needed files.
The script are designed to be run in the UCVMC/largefiles dirctory
First, the user runs a script to get the largefiles.
This script asks user which model should be downloaded then the selected model
files and other large files are copied from USC into the local directory.
./get_large_files.py
== We may copy these from my account to speed up the download
Second, the user runs a script to confirm the largefiles are intact.
This script prints out the number of OK files and the number of files with errors.
If any files have errors, those files should be re-downloaded.
./check_largefiles_md5.py
Third, the user runs the stage_files script:
This copies the files from the largefiles directory into the ucvm directory tree
./stage_large_files.py
Finally, the user moves out of the UCVMC/largefiles directory, into the UCVM home directory.
From the UCVM/ home directory, the user runs:
./ucvm_setup.py
This will run the configure, make, install commands to build the libraries and models.
13) give src directory as /project/scec_608/<username>/ucvm_src
14) give bin directory as /project/scec_608/<username>/ucvm_bin
15) Confirm entry in .bash_profile has Setup path
env | grep ucvm
env | grep UCVM
16) move to /home1/<username>/test_ucvm
list the installed modules
ucvm_query -H
ucvm_query with a list of lon-lat-depth in a file
ucvm_query -f /project/username/ucvm_bin/conf/ucvm.conf -m cvmsi < /project/username/ucvm_bin/tests/inputs/test_latlons.txt
== Terminal Message to User - Successful Installation Completes ==
<pre>
Done installing UCVM!
Thank you for installing UCVM.
Log out log back
%ucvm_query -H
Once you have set these environment variables, return to the UCVM source directory and type
make check
This will run the UCVM unit and acceptance tests. If all tests pass. UCVM is correctly installed
and ready to use on your computer.
To try out ucvm, once the tests pass, move to the UCVM installation directory, and run an example query.
As an example, you can run ucvm_query:
cd /project/scec_608/chukwueb/ucvm_bin
./bin/ucvm_query -f ./conf/ucvm.conf -m cvms < ./tests/inputs/test_latlons.txt
You will then see the following output:
Using Geo Depth coordinates as default mode.
-118.0000 34.0000 0.000 280.896 390.000 cvms 696.491 213.000 1974.976 none 0.000 0.000 0.000 crust 696.491 213.000 1974.976
-118.0000 34.0000 50.000 280.896 390.000 cvms 1669.540 548.000 2128.620 none 0.000 0.000 0.000 crust 1669.540 548.000 2128.620
-118.0000 34.0000 100.000 280.896 390.000 cvms 1683.174 603.470 2130.773 none 0.000 0.000 0.000 crust 1683.174 603.470 2130.773
-118.0000 34.0000 500.000 280.896 390.000 cvms 3097.562 1656.495 2354.105 none 0.000 0.000 0.000 crust 3097.562 1656.495 2354.105
-118.0000 34.0000 1000.000 280.896 390.000 cvms 3660.809 2056.628 2443.042 none 0.000 0.000 0.000 crust 3660.809 2056.628 2443.042
Installation complete. Installation log file saved at ./setup_log.sh
After Install Completes
- which ucvm_query’ to see if your environment is setup
- source conf/ucvm_env.sh script from either install directory or source directory
- ucvm_query -H
- installed_models.py
(base) [maechlin@discovery2 ~]$ installed_models.py [b'1d', b'bbp1d', b'cvms', b'cvmh', b'cencal', b'cvmsi', b'albacore', b'cvms5', b'cca', b'cs173', b'cs173h']
- Now, you can delete src directory if you do not plan to review, modify UCVM source code, or debug UCVM software. Deleting it saves about 150GB of disk storage if you were doing a complete install of all models.
- goto <install>/tests directory: CARC: /project/maechlin_162/ucvm_bin/tests
- ./run-testing
/project/maechlin_162/ucvm_bin/tests (base) [maechlin@discovery2 tests]$ ./run-testing Test: UCVM lib initialization PASS Test: UCVM lib add model 1D PASS Test: UCVM lib query 1D PASS Test: UCVM lib get model label 1D PASS Test: UCVM lib setparam querymode geo-depth 1D PASS Test: UCVM lib setparam querymode geo-elev 1D PASS Test: UCVM lib model version 1D PASS Test: UCVM lib add model USGS CenCal PASS Test: UCVM lib add model SCEC CVM-H PASS Test: UCVM lib add model SCEC CVM-S PASS Test: UCVM lib add model SCEC CVM-SI PASS Test: UCVM lib add model CVMS5 PASS Test: UCVM lib add model CCA PASS Test: UCVM lib add model CS173 WARNING: Could not load model into memory. Reading the model from the hard disk may result in slow performance. PASS Test: UCVM lib add model CS173H WARNING: Could not load model into memory. Reading the model from the hard disk may result in slow performance. PASS Test: ucvm library 1d model w/ large grid PASS Runnning test test_ssh_generate [SUCCESS] Runnning test test_vs30_query [SUCCESS] Running examples_api query_1d_gtl [SUCCESS] Running examples_programs_basin z2500 basin_query_cvmh [SUCCESS] Running examples_programs_basin z1000 basin_query_cvmh [SUCCESS] Running examples_programs_basin basin_query_mpi_cvms5 [SUCCESS] Running examples_programs_basin basin_query_mpi_complete_cencal_cvms [SUCCESS] Running examples_programs_basin basin_query_mpi_complete_cencal_cvms5 [SUCCESS] Running examples_programs_basin basin_query_mpi_complete_cencal_cvmsi [SUCCESS] Running examples_programs_ucvm ucvm_query_cvmh [SUCCESS] Running examples_programs_ucvm ucvm_query_cencal_cvms5 [SUCCESS] Running examples_programs_ucvm ucvm_query_cencal_cvms [SUCCESS] Running examples_programs_ucvm2etree ucvm2etree_cvmh [SUCCESS] Running examples_programs_ucvm2mesh ucvm2mesh_cvmh [SUCCESS] Running examples_programs_mesh ucvm2mesh_mpi_cvmh [SUCCESS] Running examples_programs_mesh ucvm2mesh_mpi_cvmsi [SUCCESS] Running examples_programs_mesh ucvm2mesh_mpi_layer_cvmsi [SUCCESS] Running examples_programs_mesh ucvm2mesh_mpi_layer_cvms [SUCCESS]
Testing Notes
- Testing on CARC discovery:
- Download onto /project filesystem - 20 minutes
- Compiled on headnode - 20 minutes
- Tests run on headnode - 20 minutes
Test Additions
Confirm each commmand line parameter
(base) [maechlin@discovery2 ~]$ ucvm_query -H
Usage: ucvm_query [-m models<:ifunc>] [-p user_map] [-c coordtype] [-f config] [-z zmin,zmax] [-b] < file.in
Flags:
-h This help message.
-H Detail help message.
-m Comma delimited list of crustal/GTL models to query in order
of preference. GTL models may optionally be suffixed with ':ifunc'
to specify interpolation function.
-c Z coordinate mode: geo-depth (gd, default), geo-elev (ge).
-f Configuration file. Default is ./ucvm.conf.
-p User-defined map to use for elevation and vs30 data.
-v Display model version information only.
-z Optional depth range for gtl/crust interpolation.
-b Optional output in json format
-l Optional input lon,lat,Z(depth/elevation)
Input format is:
lon lat Z
Output format is:
lon lat Z surf vs30 crustal cr_vp cr_vs cr_rho gtl gtl_vp gtl_vs gtl_rho cmb_algo cmb_vp cmb_vs cmb_rho
Notes:
- If running interactively, type Cntl-D to end input coord list.
Version: 19.4.0
Installed Resources:
1d : crustal model
bbp1d : crustal model
cmuetree : crustal model
1dgtl : gtl
elygtl : gtl
cvms : crustal model
cvmh : crustal model
cencal : crustal model
cvmsi : crustal model
albacore : crustal model
cvms5 : crustal model
cca : crustal model
cs173 : crustal model
cs173h : crustal model
linear : ifunc
ely : ifunc
ucvm : map
yong : map
model_etree : model i/f
model_patch : model i/f
map_etree : map i/f
