phreeqc3's People
phreeqc3's Issues
Fixup master/develop branches
Need to reset master/main to point to the latest release 84971d3 (tag: v3.7.3)
Some tests are failing due to time limits
Timed out @ 15 minutes on Darwin
mytest.current_analytical 484086c
Timed out @ 10 minutes on Linux
examples.ex15
examples.ex15a
examples.ex15b
mytest.colloid_U
mytest.ex15.cvode
Visual Studio before 2015 doesn't implement snprintf
for possible fix see:
https://stackoverflow.com/questions/2915672/snprintf-and-visual-studio-2010
numdiff: PR_error_incremental_101.sel: No such file or directory
CMakeLists.txt is missing PR_error_incremental
Missing database file causes infinite loop in ctest
see https://github.com/usgs-coupled/phreeqc3/actions/runs/3860140795
test (macos-latest):
https://github.com/usgs-coupled/phreeqc3/actions/runs/3860140795/jobs/6580305486#step:6:924
macos-latest was the only job to finish but also created a 3.75 GB artifact. The results weren't posted to
https://my.cdash.org/index.php?project=phreeqc3.
probably rejected due to size.
Strange results for mytest/P_Vm
Results of running tag v3.7.3 version of mytest/P_Vm:
old.zip
Results of running 421faf6 version of mytest/P_Vm:
new.zip
each folder contains the output of each of the following:
phreeqc-3.7.3-15968-x64/ original windows distribution
421faf60/ compiled from 421faf60 commit (latest version)
v3.7.3/ compiled using the same source as the distribution (using 421faf60 cmake files)
- phreeqc-3.7.3-15968-x64 fails to run newer version of P_Vm
- except for timing, both of the cmake builds yield the same results for each input file on Windows (vs2019)
replace sprintf with snprintf
check ThermoChimie7d_sit_JUNE_2011.dat encoding
google says numdiff download contains virus
Move phreeqc-chm-windows-git to github-actions
This issue was moved from usgs-coupled-subtrees/phreeqc3-HTMLversion#1
Merge conflicts #2408420
Running with gitlab-runner 15.10.1 (dcfb4b66)
on chs-shared-runners-i-046ce0ed6313[2](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L2)6747 [3](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L3)dxCawZT, system ID: s_2635aaf9f0a1
Preparing the "docker+machine" executor
00:07
Using Docker executor with image code.chs.usgs.gov:5001/coupled/containers/buildpack-deps:bionic-scm ...
Authenticating with credentials from job payload (GitLab Registry)
Pulling docker image code.chs.usgs.gov:5001/coupled/containers/buildpack-deps:bionic-scm ...
Using docker image sha256:cbed96d2ebf25728c8b52b136ad931[4](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L4)cc1dabb3b82f97c633beb27d7b3786b80 for code.chs.usgs.gov:[5](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L5)001/coupled/containers/buildpack-deps:bionic-scm with digest code.chs.usgs.gov:5001/coupled/containers/buildpack-deps@sha25[6](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L6):4b53[7](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L7)16f1b6f2bd3039707fa25a200b793825825f4f7d1adb4e3d534ac0d9d0d ...
Preparing environment
00:01
Running on runner-3dxcawzt-project-4256-concurrent-0 via runner-3dxcawzt-gitlab-runner-1681144741-cbf8231d...
Getting source from Git repository
00:24
Fetching changes with git depth set to 50...
Initialized empty Git repository in /builds/coupled/phreeqc3/.git/
Created fresh repository.
Checking out 60c6d5d0 as detached HEAD (ref is master)...
Skipping Git submodules setup
Executing "step_script" stage of the job script
01:14
Using docker image sha256:cbed96d2ebf25728c8b52b136ad9314cc1dabb3b82f97c633beb27d7b3786b80 for code.chs.usgs.gov:5001/coupled/containers/buildpack-deps:bionic-scm with digest code.chs.usgs.gov:5001/coupled/containers/buildpack-deps@sha256:4b53716f1b6f2bd3039707fa25a200b793825825f4f7d1adb4e3d534ac0d9d0d ...
$ eval $(ssh-agent -s)
Agent pid 14
$ echo "${SSH_PRIVATE_KEY_ENC}" | base64 --decode | tr -d '\r' | ssh-add -
Identity added: (stdin) ([email protected])
$ mkdir -p ~/.ssh
$ chmod 700 ~/.ssh
$ ssh-keyscan ${CI_SERVER_HOST} >> ~/.ssh/known_hosts
# code.chs.usgs.gov:22 SSH-2.0-OpenSSH_7.4
# code.chs.usgs.gov:22 SSH-2.0-OpenSSH_7.4
# code.chs.usgs.gov:22 SSH-2.0-OpenSSH_7.4
$ chmod 644 ~/.ssh/known_hosts
$ git config --global user.email "[email protected]"
$ git config --global user.name "Darth Vader"
$ cd ..
$ rm -rf ${CI_PROJECT_NAME}
$ git clone git@${CI_SERVER_HOST}:${CI_PROJECT_PATH}.git
Cloning into 'phreeqc3'...
Warning: Permanently added the ECDSA host key for IP address '10.12.1.165' to the list of known hosts.
remote: warning: ignoring extra bitmap file: '/var/opt/gitlab/git-data/repositories/@pools/[9](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L9)c/fd/9cfd3c755be26b4e1645918e2a64a26e3d851ede421e0b257f783b443bc443d1.git/objects/pack/multi-pack-index'
Checking out files: 100% (3494/3494), done.
$ cd ${CI_PROJECT_NAME}
$ #!/bin/bash -ex # collapsed multi-line command
remote: warning: ignoring extra bitmap file: '/var/opt/gitlab/git-data/repositories/@pools/aa/e0/aae02129362d611717b6c00ad8d73bf820a0f6d88fca8e515cafe78d3a335965.git/objects/pack/multi-pack-index'
From code.chs.usgs.gov:coupled/subtrees/phreeqc3-doc
* branch master -> FETCH_HEAD
Subtree is already at commit c3ed55b0e443c4ea3b85ecfc4fd8c78416a53321.
From code.chs.usgs.gov:coupled/subtrees/phreeqc3-HTMLversion
* branch master -> FETCH_HEAD
Subtree is already at commit ca6d59b0762e50d66ffbea82f9a63666bf573312.
From code.chs.usgs.gov:coupled/subtrees/phreeqc3-database
* branch master -> FETCH_HEAD
Subtree is already at commit 91aa5fd89b2f211b1dc85020c227df1a35676318.
remote: warning: ignoring extra bitmap file: '/var/opt/gitlab/git-data/repositories/@pools/43/c7/43c727ee4fc7250574d2ef90cfa16626388a10e1b30d36ece1c272953ad2ed9e.git/objects/pack/multi-pack-index'
From code.chs.usgs.gov:coupled/subtrees/phreeqc3-src
* branch master -> FETCH_HEAD
Auto-merging src/tally.cpp
CONFLICT (content): Merge conflict in src/tally.cpp
Auto-merging src/spread.cpp
CONFLICT (content): Merge conflict in src/spread.cpp
Auto-merging src/prep.cpp
CONFLICT (content): Merge conflict in src/prep.cpp
Auto-merging src/pitzer.cpp
CONFLICT (content): Merge conflict in src/pitzer.cpp
Auto-merging src/model.cpp
CONFLICT (content): Merge conflict in src/model.cpp
Auto-merging src/gases.cpp
CONFLICT (content): Merge conflict in src/gases.cpp
Auto-merging src/cl1.cpp
Automatic merge failed; fix conflicts and then commit the result.
Cleaning up project directory and file based variables
00:01
ERROR: Job failed: exit code 1
tests 258 and 338 fail on macOS
$ ctest -C Release -I 1,1,1,258,338
Test project /Users/charlton/source/repos/coupled/phreeqc3/_build
Start 1: ex1
1/3 Test #1: ex1 .............................. Passed 0.04 sec
Start 258: mytest.P_Vm
2/3 Test #258: mytest.P_Vm ......................***Failed 0.23 sec
Start 338: mytest.rho_H3PO4
3/3 Test #338: mytest.rho_H3PO4 .................***Failed 0.04 sec
33% tests passed, 2 tests failed out of 3
Total Test time (real) = 0.34 sec
The following tests FAILED:
258 - mytest.P_Vm (Failed)
338 - mytest.rho_H3PO4 (Failed)
Errors while running CTest
Output from these tests are in: /Users/charlton/source/repos/coupled/phreeqc3/_build/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.
Files
Update subtree splitting and merging for main/develop branches
Test on coupled-test (set ${GROUP} to coupled-test)???
Convert to github actions ???
on code.chs.usgs.gov (Gitlab)
rename master to main for all pipeline repos
copy main to develop for all pipeline repos
update all .gitlab-ci.yml to work on the develop branch only
mytest/current_analytical_101.sel isn't checked in
mytest/current_analytical_101.sel hasn't been checked in although
current_analytical creates it
Valgrind-Conditional jump or move depends on uninitialised value (SC)
See https://my.cdash.org/builds/2540111/dynamic_analysis
Variable SC is uninitialized when H+ is defined as H3O+ (iso.dat).
CDash warning links don't work
see:
https://my.cdash.org/viewBuildError.php?type=1&buildid=2267338
and note that the file:line_no links yields a 404 error:
https://github.com/usgs-coupled/phreeqc3/blob/master/print.cpp#L1461
but it should be:
https://github.com/usgs-coupled/phreeqc3/blob/master/src/print.cpp#L1461
might be able to fix by modifying the way source files are included in the
CMakeLists.txt files
Consider using cmake-format cmake-lint for pre-commits
Add database/PHREEQC_ThermoddemV1.10_15Dec2020.dat to dist
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