src issueshttps://gitlab.psi.ch/OPAL/src/-/issues2023-07-24T11:00:49+02:00https://gitlab.psi.ch/OPAL/src/-/issues/750Trimcoil implementation bug2023-07-24T11:00:49+02:00snuverink_jjochem.snuverink@psi.chTrimcoil implementation bug### Summary
In #276 and !53 a trim coil range in the azimuthal direction was introduced. However, this was not properly tested and it contained a bug, that was discovered by @zhang_h. This was partly fixed in #736 / !598, but not comple...### Summary
In #276 and !53 a trim coil range in the azimuthal direction was introduced. However, this was not properly tested and it contained a bug, that was discovered by @zhang_h. This was partly fixed in #736 / !598, but not completely tested.
### What is the current *bug* behavior?
The trim coils do not work anymore without `PHIMIN` and `PHIMAX` specified.
### What is the expected *correct* behavior?
Trim coils working as normal.
### Possible fixes
The bug was introduced in 77c975dcca3b99cf195cbf020d5039f8be745646, especially the default value of `PHIMAX` was not specified (https://gitlab.psi.ch/OPAL/src/-/commit/77c975dcca3b99cf195cbf020d5039f8be745646#fa26d1e4b267fcc893fcd886f40d73b50d62cdef_46_56) and the `TrimCoil::setAzimuth` method was not so well implemented (https://gitlab.psi.ch/OPAL/src/-/commit/77c975dcca3b99cf195cbf020d5039f8be745646#c96f8a350e29295ac068d6a60d9a39c1972d72e6_16_28).2023.1snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/src/-/issues/748Improve error message for using protected keywords2023-03-31T14:12:22+02:00snuverink_jjochem.snuverink@psi.chImprove error message for using protected keywordsReported by @zhang_h:
An input like:
```
ring: Cyclotron, TYPE="RING", ...;
```
will generate an error:
```
Error>
Error> *** User error detected by function "OpalData::define()"
Error> You cannot replace the object "RING".
Error...Reported by @zhang_h:
An input like:
```
ring: Cyclotron, TYPE="RING", ...;
```
will generate an error:
```
Error>
Error> *** User error detected by function "OpalData::define()"
Error> You cannot replace the object "RING".
Error> You cannot replace the object "RING".
```
This is because `ring` is a protected keyword and can't be used as an object name. However, from the user perspective this seems not very clear.
The error message comes from OpalData.cpp:
```c++
if (oldObject->isBuiltin() || ! oldObject->canReplaceBy(newObject)) {
throw OpalException("OpalData::define()",
"You cannot replace the object \"" + name + "\".");
} else {
```
I propose to make a distinction between the two cases and change it to:
```c++
if (oldObject->isBuiltin()) {
throw OpalException("OpalData::define()",
"The keyword \"" + name + "\" is protected and can't be used to name an object.");
else if (! oldObject->canReplaceBy(newObject)) {
throw OpalException("OpalData::define()",
"You cannot replace the already defined object \"" + name + "\".");
} // else not needed
```
Also it might be good not to have "name" in uppercase letters if the user writes it in lowercase, but I couldn't quickly find out where this happens.2023.1snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/src/-/issues/747OPAL hangs when running FFA in parallel2022-11-08T12:25:32+01:00ext-rogers_cOPAL hangs when running FFA in parallel### Summary
OPAL hangs when running FFA in parallel
### Possible fixes
`Ring::apply` has a call to `lossDS_m->save();` which in turn calls `ippl::allreduce`. This is a type of MPI reduce. At the same time, `ParallelCyclotronTracker::d...### Summary
OPAL hangs when running FFA in parallel
### Possible fixes
`Ring::apply` has a call to `lossDS_m->save();` which in turn calls `ippl::allreduce`. This is a type of MPI reduce. At the same time, `ParallelCyclotronTracker::deleteParticle` calls `allreduce(flagNeedUpdate, 1, std::logical_or<bool>());`. So the procs can never align and we get a hang.
Fix is to call `lossDS_m->save()` in the Ring::finalise method, which seems to be the approach taken by `Cyclotron`.2023.1ext-rogers_cext-rogers_chttps://gitlab.psi.ch/OPAL/src/-/issues/745PyOPAL - FFA lattice2023-04-20T16:54:05+02:00ext-rogers_cPyOPAL - FFA lattice### Summary
Implement supporting code to model our current FFA lattice in PyOPAL. That means writing API for following elements:
- ScalingFFAMagnet and EndFieldModels
- DumpEMFields
- LocalCartesianOffset (other offsets?)
- Probe
- Mult...### Summary
Implement supporting code to model our current FFA lattice in PyOPAL. That means writing API for following elements:
- ScalingFFAMagnet and EndFieldModels
- DumpEMFields
- LocalCartesianOffset (other offsets?)
- Probe
- MultipoleT
- VariableRFCavity and TimeDependence plugin
- General consideration of stability/etc
Maybe some other things I forgot.
Also (of course)
- Code
- Test
I will do Documentation in a separate feature when I am more happy with the whole framework.2023.1ext-rogers_cext-rogers_chttps://gitlab.psi.ch/OPAL/src/-/issues/744Use smart pointers for fieldmaps2022-11-08T09:18:57+01:00krausUse smart pointers for fieldmaps2023.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/743Compilation fails2022-10-19T15:13:27+02:00ext-calvo_ppedro.calvo@ciemat.esCompilation failsAfter OPAL/src!602, OPAL compilation fails. The format of the new version is invalid (see [link](http://amas.web.psi.ch/opal/master/output/2022-10-19_10-49.txt))After OPAL/src!602, OPAL compilation fails. The format of the new version is invalid (see [link](http://amas.web.psi.ch/opal/master/output/2022-10-19_10-49.txt))gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/742change version in master to 2022.2-dev2022-10-19T15:11:24+02:00gsellchange version in master to 2022.2-dev2022.2gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/741change version strings for 2022.12022-10-14T13:53:10+02:00gsellchange version strings for 2022.12022.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/740Release version 2022.12023-03-30T16:12:12+02:00gsellRelease version 2022.1**source code**
* [x] review the file `src/addToDoxygenMainPage.h` (list of Authors)
* [x] create issue "Release version YEAR.N"
* [x] create branch OPAL-YEAR.N
* [x] create issue and MR with target branch YEAR.N
* [x] ...**source code**
* [x] review the file `src/addToDoxygenMainPage.h` (list of Authors)
* [x] create issue "Release version YEAR.N"
* [x] create branch OPAL-YEAR.N
* [x] create issue and MR with target branch YEAR.N
* [x] update version string in CMakeLists.txt and Doxyfile to YEAR.N
* [x] wait for approval and merge
* [x] tag version OPAL-YEAR.N.0 on branch OPAL-YEAR.N
* [x] create MR with target branch master
* [x] update version string in CMakeLists.txt and Doxyfile to YEAR.N+1-dev
* [x] wait for approval and merge
**binaries**
* [x] upload source tar-ball to <br>
`/afs/psi.ch/project/amas/webhosting/Downloads/OPAL/src/OPAL-YEAR.N.0.tar.xz`
* [x] binary for Linux
* [x] compile on opalrunner with build-recipes <br>
Note:
* [x] upload Linux binary package to <br>
`/afs/psi.ch/project/amas/webhosting/Downloads/OPAL/package/OPAL-YEAR.N.0-1-x86_64-linux.tar.xz`
* [x] tested by other developers
* [x] binary for macOS x86_64
* [x] compile with Clang on macOS with Intel CPU and current OS/Xcode
* [x] upload macOS binary package to <br>
`/afs/psi.ch/project/amas/webhosting/Downloads/OPAL/package/OPAL-YEAR.N.0-1-x86_64-macos.tar.xz`
* [x] tested by other developers
* [x] binary for macOS M1
* [x] compile with Clang on macOS with M1 CPU and current OS/Xcode
* [x] upload macOS binary package to <br>
`/afs/psi.ch/project/amas/webhosting/Downloads/OPAL/package/OPAL-YEAR.N.0-1-arm-macos.tar.xz`
* [x] tested by other developers
**regression-tests**
* [x] create new branch YEAR.N
* [x] setup the regression-tests to run the new version on opalrunner.psi.ch
**manual/documentation**
* [x] setup a new branch for the new version of the manual
* [x] fix version, branches and links in `Manual.attributes`
* [x] clone repository into <br>
`/afs/psi.ch/project/amas/webhosting/opal/Documentation/YEAR.N` <br>
and checkout new branch: <br>
`git clone https://gitlab.psi.ch/OPAL/documentation/manual.git YEAR.N && cd YEAR.N && git checkout OPAL-YEAR.N`
* [x] add links to the binaries in the wiki
* [x] update https://gitlab.psi.ch/OPAL/src/wikis/For-Developers/Compile-OPAL
* [x] compile the change log/release notes and publish it in the wiki: https://gitlab.psi.ch/OPAL/src/wikis/ReleaseNotes
* [x] build Doxygen documentation
* [x] update https://gitlab.psi.ch/OPAL/src/wikis/home
**tracker**
* [x] new milestone for `OPAL x.(y+1)`
* [x] update labels and milestones in issues
**varia**
* [x] PSI module
* [x] write e-mail to mailing list2022.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/739fixes for compilation on macOS2022-09-30T22:11:38+02:00gsellfixes for compilation on macOS2022.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/738Fix some uninitialized variables2022-09-21T15:16:30+02:00muralikrishnanFix some uninitialized variablesSome of the newly added quantities such as temperature, DebyeLength and plasma parameter in the stat file were uninitialized. Since during emission we do not compute them this may cause an issue.Some of the newly added quantities such as temperature, DebyeLength and plasma parameter in the stat file were uninitialized. Since during emission we do not compute them this may cause an issue.2022.1muralikrishnanmuralikrishnanhttps://gitlab.psi.ch/OPAL/src/-/issues/737P3M solver2022-09-23T12:59:37+02:00muralikrishnanP3M solver### Summary
Complete the P3M solver initiated by Benjamin Ulmer in his Master's thesis so that it can be used in
scenarios where collisions might be important.### Summary
Complete the P3M solver initiated by Benjamin Ulmer in his Master's thesis so that it can be used in
scenarios where collisions might be important.2022.1muralikrishnanmuralikrishnanhttps://gitlab.psi.ch/OPAL/src/-/issues/736Trimcoil implementation bug2023-02-13T15:50:53+01:00snuverink_jjochem.snuverink@psi.chTrimcoil implementation bug### Summary
In #276 and !53 a trim coil range in the azimuthal direction was introduced. However, this was not properly tested and it contained a bug, that was discovered by @zhang_h.
### What is the current *bug* behavior?
The trim c...### Summary
In #276 and !53 a trim coil range in the azimuthal direction was introduced. However, this was not properly tested and it contained a bug, that was discovered by @zhang_h.
### What is the current *bug* behavior?
The trim coils do not work anymore.
### What is the expected *correct* behavior?
Trim coils working as normal.
### Possible fixes
The bug was introduced in 77c975dcca3b99cf195cbf020d5039f8be745646, specifically in line
https://gitlab.psi.ch/OPAL/src/-/blob/160558d02705876d15775fe7527227a142bc2088/src/Classic/AbsBeamline/Cyclotron.cpp#L101
the order of the arguments is wrong, see also https://gitlab.psi.ch/OPAL/src/-/blob/0601ed262da6cd29690abff38053c900f9bafacc/src/Classic/TrimCoils/TrimCoil.cpp#L432022.1snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/src/-/issues/735Index error when reading wake function from sdds file2022-10-11T07:57:43+02:00adelmannIndex error when reading wake function from sdds fileIn the sdds file N lines are specified, so the loop
need to go from 0 to N-1 but does go to NIn the sdds file N lines are specified, so the loop
need to go from 0 to N-1 but does go to N2022.1adelmannadelmannhttps://gitlab.psi.ch/OPAL/src/-/issues/734SDDS wake function read error2022-09-14T11:28:20+02:00adelmannSDDS wake function read errorError>
Error> *** User error detected by function "Attributes::getString()"
Error> Attribute "FNAME" is not string.
Error> Attribute "FNAME" is not string.
application called MPI_Abort(MPI_COMM_WORLD, -100) - process 0
[unset]: ...Error>
Error> *** User error detected by function "Attributes::getString()"
Error> Attribute "FNAME" is not string.
Error> Attribute "FNAME" is not string.
application called MPI_Abort(MPI_COMM_WORLD, -100) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=-100
wakecorr: WAKE, TYPE="LONG-SHORT-RANGE", NBIN=500, FNAME="testWake220GHz.sdds" ;2022.1https://gitlab.psi.ch/OPAL/src/-/issues/733minor code cleanup2022-09-14T11:28:02+02:00gsellminor code cleanup* remove commented out source code
* don't include files which are not used
* ...* remove commented out source code
* don't include files which are not used
* ...2022.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/732fix Apple Clang warnings2022-09-14T11:27:49+02:00gsellfix Apple Clang warningsApple Clang 13 on Apple Silicon complains about several minor issue like unused variables, missing override declarations etc.Apple Clang 13 on Apple Silicon complains about several minor issue like unused variables, missing override declarations etc.2022.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/731minor fixes in the main CMake configuration file2022-09-14T11:27:31+02:00gsellminor fixes in the main CMake configuration fileApple Clang doesn't support OpenMP: add check
If we compile with Clang, Fortran is not available (Flang is not yet production ready)Apple Clang doesn't support OpenMP: add check
If we compile with Clang, Fortran is not available (Flang is not yet production ready)2022.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/730OPAL (master) gives a segfault when ending2022-09-14T11:29:06+02:00ext-piot_pOPAL (master) gives a segfault when ending### Summary
The most recent master version compiles fine on fedora fc35 but it gives a segfault upon finishing
A checkout of the OPAL-2011-1 compile on the same distro works just fine.
### Steps to reproduce the failure
git check out ...### Summary
The most recent master version compiles fine on fedora fc35 but it gives a segfault upon finishing
A checkout of the OPAL-2011-1 compile on the same distro works just fine.
### Steps to reproduce the failure
git check out
git checkout master
cd ../master
CC=mpicc CXX=mpicxx cmake ../src/ -DHDF5_C_COMPILER_EXECUTABLE=/usr/lib64/openmpi/bin/h5pcc -D CMAKE_BUILD_TYPE=Release -D CMAKE_CXX_FLAGS="-Wno-error=cast-function-type -Wno-cast-function-type -Wl,--copy-dt-needed-entries"
make -j 24
cd ../example
mpirun -np 8 ../master/src/opal awaDrive_all.in
### What is the current *bug* behavior?
```
Timings{0}> WakeField........... Wall max = 0, CPU max = 0
Timings{0}> Wall avg = 0, CPU avg = 0
Timings{0}> Wall min = 0, CPU min = 0
Timings{0}>
Timings{0}> Write H5-File....... Wall max = 2.27603, CPU max = 1.23
Timings{0}> Wall avg = 2.27519, CPU avg = 1.115
Timings{0}> Wall min = 2.27071, CPU min = 1.03
Timings{0}>
Timings{0}> Write Stat.......... Wall max = 0.105094, CPU max = 0.07
Timings{0}> Wall avg = 0.0356317, CPU avg = 0.02625
Timings{0}> Wall min = 0.0245887, CPU min = 0
Timings{0}>
Timings{0}> -----------------------------------------------------------------
[localhost:356319:0:356319] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[localhost:356320:0:356320] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[localhost:356318:0:356318] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
[localhost:356321:0:356321] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace (tid: 356320) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2a4) [0x7f1d48c29864]
1 /lib64/libucs.so.0(+0x2a41d) [0x7f1d48c2d41d]
2 /lib64/libucs.so.0(+0x2a5fa) [0x7f1d48c2d5fa]
3 opal() [0xc8f6c0]
4 opal() [0x910701]
5 opal() [0x7eb18c]
6 opal() [0xb935d9]
7 opal() [0x918acf]
8 opal() [0xa1a7af]
9 opal() [0x72c16a]
10 opal() [0x72c189]
11 opal() [0x6f368a]
12 /lib64/libc.so.6(+0x57a15) [0x7f1d4d257a15]
13 /lib64/libc.so.6(on_exit+0) [0x7f1d4d257b90]
14 /lib64/libc.so.6(+0x40447) [0x7f1d4d240447]
15 /lib64/libc.so.6(__libc_start_main+0x80) [0x7f1d4d2404f0]
16 opal() [0x4abbd5]
=================================
==== backtrace (tid: 356319) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2a4) [0x7fa60d660864]
1 /lib64/libucs.so.0(+0x2a41d) [0x7fa60d66441d]
2 /lib64/libucs.so.0(+0x2a5fa) [0x7fa60d6645fa]
3 opal() [0xc8f6c0]
4 opal() [0x910701]
5 opal() [0x7eb18c]
6 opal() [0xb935d9]
7 opal() [0x918acf]
```
### What is the expected *correct* behavior?
git check out git checkout OPAL-2011-1
cd ../OPAL-2011-1
CC=mpicc CXX=mpicxx cmake ../src/ -DHDF5_C_COMPILER_EXECUTABLE=/usr/lib64/openmpi/bin/h5pcc -D CMAKE_BUILD_TYPE=Release -D CMAKE_CXX_FLAGS="-Wno-error=cast-function-type -Wno-cast-function-type -Wl,--copy-dt-needed-entries"
make -j 24
cd ../example
mpirun -np 8 ../OPAL-2011-1/src/opal awaDrive_all.in
works fine
### Relevant logs and/or screenshots
the input file I use are the AWA photoinjector; the specific version is available at https://xgitlab.cels.anl.gov/awa/awa-opal-lattices2022.1https://gitlab.psi.ch/OPAL/src/-/issues/729dumping 6D beam matrix at each time steps2022-09-23T12:59:28+02:00ext-piot_pdumping 6D beam matrix at each time steps### Summary
Introduce an option dumpBeamMarix that enable the 21 elements (upper triangle) of the 6D beam (sigma) matrix to be written in the stat file.### Summary
Introduce an option dumpBeamMarix that enable the 21 elements (upper triangle) of the 6D beam (sigma) matrix to be written in the stat file.2022.1ext-piot_pext-piot_p