src issueshttps://gitlab.psi.ch/OPAL/src/-/issues2021-10-13T09:30:38+02:00https://gitlab.psi.ch/OPAL/src/-/issues/641UndulatorAWA-Test yielding different results2021-10-13T09:30:38+02:00krausUndulatorAWA-Test yielding different resultsAfter implementing OPAL/src#503 the UndulatorAWA-Test yields slightly different results.After implementing OPAL/src#503 the UndulatorAWA-Test yields slightly different results.OPAL 2021.1krausalbajacas_aarnau.albajacas@psi.chkraushttps://gitlab.psi.ch/OPAL/src/-/issues/640Update time unit in loss output file of some elements2021-03-24T09:09:01+01:00ext-calvo_ppedro.calvo@ciemat.esUpdate time unit in loss output file of some elementsFrom a [discussion](https://gitlab.psi.ch/OPAL/src/-/merge_requests/477#note_30392) on MR !477, and in agreement with #357, the unit of time should be unified to `s` in some elements to avoid inconsistencies in the `LossDataSink` output ...From a [discussion](https://gitlab.psi.ch/OPAL/src/-/merge_requests/477#note_30392) on MR !477, and in agreement with #357, the unit of time should be unified to `s` in some elements to avoid inconsistencies in the `LossDataSink` output file.OPAL 2021.1ext-calvo_ppedro.calvo@ciemat.esext-calvo_ppedro.calvo@ciemat.eshttps://gitlab.psi.ch/OPAL/src/-/issues/639unused variable in ippl/test/particle/p3m3dMicrobunching.cpp2021-03-23T09:39:02+01:00gsellunused variable in ippl/test/particle/p3m3dMicrobunching.cppCompilation fails with an `unused variable` warning in `ippl/test/particle/p3m3dMicrobunching.cpp` if compile type is set to `Release`.Compilation fails with an `unused variable` warning in `ippl/test/particle/p3m3dMicrobunching.cpp` if compile type is set to `Release`.OPAL 2021.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/638Fix algorithm for computation of standard deviation2021-10-13T09:30:21+02:00krausFix algorithm for computation of standard deviationFrom a discussion on MR 477 (https://gitlab.psi.ch/OPAL/src/-/merge_requests/477#note_30754):
> I think the equation for stdTime_m is not correct. It should be std::sqrt((localMoments[l++] - totalNumParticles_m *
> std::pow(meanTime_m, ...From a discussion on MR 477 (https://gitlab.psi.ch/OPAL/src/-/merge_requests/477#note_30754):
> I think the equation for stdTime_m is not correct. It should be std::sqrt((localMoments[l++] - totalNumParticles_m *
> std::pow(meanTime_m, 2)) * perParticle). However, this way of calculating can be numerically unstable (see also
> https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance).
>
> I usually do a double loop, but that might be not so easy here. Perhaps with "Computing shifted data" with the first value
> taken as preliminary mean (this seems valid since the particle times are not expected to lie very far away from each other,
> or Welford's algorithm can be tried?OPAL 2021.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/637Segmantation fault with BoundaryGeometry2021-02-17T11:21:51+01:00ext-calvo_ppedro.calvo@ciemat.esSegmantation fault with BoundaryGeometrySince MR OPAL/src!464, I got a segmentation fault running opal-cycl with geometry
```
*** Process received signal ***
Signal: Aborted (6)
Signal code: (-6)
[ 0] /lib64/libpthread.so.0[0x30b520f130]
[ 1] /lib64/libc.so.6(gsignal+0x39)[0...Since MR OPAL/src!464, I got a segmentation fault running opal-cycl with geometry
```
*** Process received signal ***
Signal: Aborted (6)
Signal code: (-6)
[ 0] /lib64/libpthread.so.0[0x30b520f130]
[ 1] /lib64/libc.so.6(gsignal+0x39)[0x30b4a359d9]
[ 2] /lib64/libc.so.6(abort+0x148)[0x30b4a370e8]
[ 3] opal(_ZNSt6vectorIN7Message7MsgItemESaIS1_EE7reserveEm+0x0)[0x64af30]
[ 4] opal[0x80121b]
[ 5] opal(_ZN16BoundaryGeometry10initializeEv+0x2e62)[0x8044e2]
[ 6] opal(_ZN16BoundaryGeometryC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPS_+0x348)[0x805468]
[ 7] opal(_ZN16BoundaryGeometry5cloneERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x25)[0x8055e5]
[ 8] opal(_ZN8TrackRun21setupCyclotronTrackerEv+0xeb0)[0x81ea60]
[ 9] opal(_ZN8TrackRun7executeEv+0xc8)[0x8211d8]
[10] opal(_ZNK10OpalParser7executeEP6ObjectRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x3a)[0x6f197a]
[11] opal(_ZNK10OpalParser11parseActionER9Statement+0xfd)[0x6f5ced]
[12] opal(_ZNK10OpalParser5parseER9Statement+0x173)[0x6f4933]
[13] opal(_ZNK10OpalParser3runEv+0x4e)[0x6f214e]
[14] opal(_ZN8TrackCmd7executeEv+0x97c)[0x81b50c]
[15] opal(_ZNK10OpalParser7executeEP6ObjectRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x3a)[0x6f197a]
[16] opal(_ZNK10OpalParser11parseActionER9Statement+0xfd)[0x6f5ced]
[17] opal(_ZNK10OpalParser5parseER9Statement+0x173)[0x6f4933]
[18] opal(_ZNK10OpalParser3runEv+0x4e)[0x6f214e]
[19] opal(_ZNK10OpalParser3runEP11TokenStream+0x70)[0x6f6260]
[20] opal(main+0x1f5d)[0x6443cd]
[21] /lib64/libc.so.6(__libc_start_main+0xf5)[0x30b4a21b45]
[22] opal[0x6356a9]
```
cc: @kraus, @gsellOPAL 2021.1https://gitlab.psi.ch/OPAL/src/-/issues/636Loss files overwritten for collimators2021-02-08T13:30:30+01:00ext-calvo_ppedro.calvo@ciemat.esLoss files overwritten for collimatorsThe particles hitting the collimator and lost particles by energy loss in the material are saved in the same file because the file name are equal.
Renaming the file for lost particles by particle-matter interactions according to the lab...The particles hitting the collimator and lost particles by energy loss in the material are saved in the same file because the file name are equal.
Renaming the file for lost particles by particle-matter interactions according to the label of `PARTICLEMATTERINTERACTION` command, we'll be able to distinguish both casesOPAL 2021.1ext-calvo_ppedro.calvo@ciemat.esext-calvo_ppedro.calvo@ciemat.eshttps://gitlab.psi.ch/OPAL/src/-/issues/635Get correct output of VALUE, OPTION->AUTOPHASE2021-10-13T09:30:59+02:00krausGet correct output of VALUE, OPTION->AUTOPHASEWhen querying the value of Options the user gets the default value but not the actual value. E.g. after
```
OPTION, AUTOPHASE=4;
VALUE, OPTION->AUTOPHASE;
```
one would expect to get
```
value: {OPTION->AUTOPHASE} = {4}
```
as output. B...When querying the value of Options the user gets the default value but not the actual value. E.g. after
```
OPTION, AUTOPHASE=4;
VALUE, OPTION->AUTOPHASE;
```
one would expect to get
```
value: {OPTION->AUTOPHASE} = {4}
```
as output. But this isn't the case.OPAL 2021.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/633Renaming particle matter interactions models and types2021-02-09T15:26:02+01:00ext-calvo_ppedro.calvo@ciemat.esRenaming particle matter interactions models and typesFollowing [discussion](https://gitlab.psi.ch/OPAL/src/-/merge_requests/466#note_29427) from !466, the types of Particle Matter Interactions should be the name of the physics models. Then, `CollimatorPhysics` will be renamed as `Scatterin...Following [discussion](https://gitlab.psi.ch/OPAL/src/-/merge_requests/466#note_29427) from !466, the types of Particle Matter Interactions should be the name of the physics models. Then, `CollimatorPhysics` will be renamed as `ScatteringPhysics`.
I also propose to rename `BeamStripping` element as `Vacuum` in order to use more intuitive element names
This issue involve updating some regression-tests (see OPAL/regression-tests#101)OPAL 2021.1ext-calvo_ppedro.calvo@ciemat.esext-calvo_ppedro.calvo@ciemat.eshttps://gitlab.psi.ch/OPAL/src/-/issues/632Delete particles that move in the opposite direction than the bunch.2021-04-05T20:09:26+02:00krausDelete particles that move in the opposite direction than the bunch.### Summary
When running some simulations a drastic increase in overall compute time is noticed. This seems to originate from the evaluation of external fields.
### Steps to reproduce
Run the same simulation with Opal 2.2 and 2.4 and...### Summary
When running some simulations a drastic increase in overall compute time is noticed. This seems to originate from the evaluation of external fields.
### Steps to reproduce
Run the same simulation with Opal 2.2 and 2.4 and compare the timings.
### What is the current *bug* behavior?
The time to evaluate the external fields has regressed from Opal 2.2.
### What is the expected *correct* behavior?
The evaluation of the external fields shouldn't take longer as in Opal 2.2
### Relevant logs and/or screenshots
Timing for Opal 2.4
```
Timings{0}> -----------------------------------------------------------------
Timings{0}> Timing results for 16 nodes:
Timings{0}> -----------------------------------------------------------------
Timings{0}> mainTimer........... Wall tot = 1333.67, CPU tot = 1304.62
Timings{0}>
Timings{0}> Binaryrepart........ Wall max = 0.0760612, CPU max = 0.12
Timings{0}> Wall avg = 0.0748878, CPU avg = 0.076875
Timings{0}> Wall min = 0.0710163, CPU min = 0.04
Timings{0}>
Timings{0}> Boundingbox......... Wall max = 21.1333, CPU max = 21.51
Timings{0}> Wall avg = 20.492, CPU avg = 20.3581
Timings{0}> Wall min = 19.5912, CPU min = 18.98
Timings{0}>
Timings{0}> Boundingbox-bounds.. Wall max = 3.31469, CPU max = 3.25
Timings{0}> Wall avg = 2.33188, CPU avg = 2.32125
Timings{0}> Wall min = 1.45284, CPU min = 1.43
Timings{0}>
Timings{0}> Boundingbox-update.. Wall max = 12.3236, CPU max = 12.66
Timings{0}> Wall avg = 12.2843, CPU avg = 12.1619
Timings{0}> Wall min = 12.2186, CPU min = 11.72
Timings{0}>
Timings{0}> Compute Statistics.. Wall max = 24.9249, CPU max = 25.18
Timings{0}> Wall avg = 23.5228, CPU avg = 23.6244
Timings{0}> Wall min = 21.6156, CPU min = 21.35
Timings{0}>
Timings{0}> ComputePotential.... Wall max = 212.61, CPU max = 213.74
Timings{0}> Wall avg = 211.029, CPU avg = 210.689
Timings{0}> Wall min = 207.543, CPU min = 207.01
Timings{0}>
Timings{0}> Create Distr........ Wall max = 0.0197351, CPU max = 0.03
Timings{0}> Wall avg = 0.0186866, CPU avg = 0.020625
Timings{0}> Wall min = 0.0185006, CPU min = 0.01
Timings{0}>
Timings{0}> External field eval. Wall max = 711.153, CPU max = 711.74
Timings{0}> Wall avg = 361.201, CPU avg = 361.191
Timings{0}> Wall min = 2.25931, CPU min = 2.35
Timings{0}>
Timings{0}> Fast inside test.... 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}> Histogram........... 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}> Initialize geometry. 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}> Inside test......... 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}> Load Distr.......... 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}> Particle Inside..... 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}> Ray tracing......... 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}> SelfField total..... Wall max = 380.273, CPU max = 380.01
Timings{0}> Wall avg = 344.384, CPU avg = 344.401
Timings{0}> Wall min = 317.067, CPU min = 318.26
Timings{0}>
Timings{0}> SF: GreensFTotal.... Wall max = 134.448, CPU max = 134.95
Timings{0}> Wall avg = 133.307, CPU avg = 132.716
Timings{0}> Wall min = 131.767, CPU min = 130.46
Timings{0}>
Timings{0}> TIntegration1....... Wall max = 20.5137, CPU max = 20.53
Timings{0}> Wall avg = 19.1446, CPU avg = 19.1488
Timings{0}> Wall min = 17.3008, CPU min = 17.47
Timings{0}>
Timings{0}> TIntegration2....... Wall max = 38.3021, CPU max = 38.52
Timings{0}> Wall avg = 36.8959, CPU avg = 36.8775
Timings{0}> Wall min = 35.997, CPU min = 35.53
Timings{0}>
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 = 49.9556, CPU max = 21.73
Timings{0}> Wall avg = 49.9353, CPU avg = 20.2519
Timings{0}> Wall min = 49.8026, CPU min = 17.74
Timings{0}>
Timings{0}> Write Stat.......... Wall max = 9.01406, CPU max = 2.07
Timings{0}> Wall avg = 0.833675, CPU avg = 0.405
Timings{0}> Wall min = 0.281822, CPU min = 0.22
Timings{0}>
Timings{0}> -----------------------------------------------------------------
```
Timing for Opal 2.2 and the same input file
```
Timings{0}> -----------------------------------------------------------------
Timings{0}> Timing results for 16 nodes:
Timings{0}> -----------------------------------------------------------------
Timings{0}> mainTimer........... Wall tot = 698.587, CPU tot = 672.33
Timings{0}>
Timings{0}> Binaryrepart........ Wall max = 0.0804251, CPU max = 0.13
Timings{0}> Wall avg = 0.0792938, CPU avg = 0.078125
Timings{0}> Wall min = 0.0762691, CPU min = 0.04
Timings{0}>
Timings{0}> Boundingbox......... Wall max = 21.9074, CPU max = 22.05
Timings{0}> Wall avg = 21.2645, CPU avg = 21.2381
Timings{0}> Wall min = 20.2972, CPU min = 19.86
Timings{0}>
Timings{0}> Boundingbox-bounds.. Wall max = 3.23519, CPU max = 3.3
Timings{0}> Wall avg = 2.29564, CPU avg = 2.33812
Timings{0}> Wall min = 1.43132, CPU min = 1.19
Timings{0}>
Timings{0}> Boundingbox-update.. Wall max = 13.0062, CPU max = 13.74
Timings{0}> Wall avg = 12.9693, CPU avg = 12.9756
Timings{0}> Wall min = 12.8177, CPU min = 12.44
Timings{0}>
Timings{0}> Compute Statistics.. Wall max = 26.1269, CPU max = 26.62
Timings{0}> Wall avg = 24.6571, CPU avg = 24.815
Timings{0}> Wall min = 22.6815, CPU min = 22.65
Timings{0}>
Timings{0}> ComputePotential.... Wall max = 221.744, CPU max = 222.57
Timings{0}> Wall avg = 219.925, CPU avg = 219.121
Timings{0}> Wall min = 215.744, CPU min = 214.95
Timings{0}>
Timings{0}> Create Distr........ Wall max = 0.0196037, CPU max = 0.03
Timings{0}> Wall avg = 0.01854, CPU avg = 0.019375
Timings{0}> Wall min = 0.0183704, CPU min = 0.01
Timings{0}>
Timings{0}> External field eval. Wall max = 83.0337, CPU max = 83.09
Timings{0}> Wall avg = 37.3202, CPU avg = 37.67
Timings{0}> Wall min = 2.13352, CPU min = 2.24
Timings{0}>
Timings{0}> Fast inside test.... 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}> Histogram........... 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}> Initialize geometry. 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}> Inside test......... 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}> Load Distr.......... 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}> Particle Inside..... 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}> Ray tracing......... 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}> Secondary emission.. 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}> SelfField total..... Wall max = 398.178, CPU max = 399.5
Timings{0}> Wall avg = 359.377, CPU avg = 358.998
Timings{0}> Wall min = 330.56, CPU min = 330.17
Timings{0}>
Timings{0}> SF: GreensFTotal.... Wall max = 140.186, CPU max = 141.31
Timings{0}> Wall avg = 139.146, CPU avg = 138.486
Timings{0}> Wall min = 137.841, CPU min = 135.62
Timings{0}>
Timings{0}> TIntegration1....... Wall max = 21.4125, CPU max = 21.77
Timings{0}> Wall avg = 20.1085, CPU avg = 19.935
Timings{0}> Wall min = 18.3236, CPU min = 18.12
Timings{0}>
Timings{0}> TIntegration2....... Wall max = 40.1375, CPU max = 40.82
Timings{0}> Wall avg = 38.7925, CPU avg = 38.8013
Timings{0}> Wall min = 37.9342, CPU min = 37.21
Timings{0}>
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 = 47.1853, CPU max = 21.09
Timings{0}> Wall avg = 47.1643, CPU avg = 18.93
Timings{0}> Wall min = 47.0338, CPU min = 15.95
Timings{0}>
Timings{0}> Write Stat.......... Wall max = 9.99641, CPU max = 3.93
Timings{0}> Wall avg = 2.74196, CPU avg = 2.36437
Timings{0}> Wall min = 2.17362, CPU min = 2.09
Timings{0}>
Timings{0}> -----------------------------------------------------------------
```OPAL 2021.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/631Verifying particle matter interaction type2021-01-18T09:27:07+01:00ext-calvo_ppedro.calvo@ciemat.esVerifying particle matter interaction type`TYPE` of particle matter interaction in the input file must be verified through an `OpalException` to prevent misallocation`TYPE` of particle matter interaction in the input file must be verified through an `OpalException` to prevent misallocationOPAL 2021.1ext-calvo_ppedro.calvo@ciemat.esext-calvo_ppedro.calvo@ciemat.eshttps://gitlab.psi.ch/OPAL/src/-/issues/630Add command line option to return git hash2021-10-13T09:31:10+02:00krausAdd command line option to return git hashOPAL 2021.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/627Add -Wp,-D_GLIBCXX_ASSERTIONS to the build flags2021-10-13T09:30:48+02:00krausAdd -Wp,-D_GLIBCXX_ASSERTIONS to the build flagsAs reported by Rob from Radiasoft (see below) Fedora (and also RHEL and derivatives?) adds "-Wp,-D_GLIBCXX_ASSERTIONS" to the build flags. This results, among other things, in checking the memory access in STL containers. In Opal we ofte...As reported by Rob from Radiasoft (see below) Fedora (and also RHEL and derivatives?) adds "-Wp,-D_GLIBCXX_ASSERTIONS" to the build flags. This results, among other things, in checking the memory access in STL containers. In Opal we often use `&someVector[0]` which can cause an assertion if the vector has no elements. Where it isn't guaranteed that the vector has elements we have to handle this situation (e.g. as in [Boost::mpi](https://www.boost.org/doc/libs/1_75_0/boost/mpi/detail/antiques.hpp) ) to avoid an assertion failure in combination with `_GLIBCXX_ASSERTIONS`.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
From: Rob Nagler <opal-rtnkh@q33.us>
Date: Tue, 22 Dec 2020 17:04:55 -0700
Subject: Re: [Opal] Compiling issues (Fedora 32/gcc10)
Ran into another issue with Fedora 32. They've turned on code hardening (
discussion
<https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org/thread/TMDJMX2OYE7Z2WHKXMOMTOBDHJKZJ3NV/>)
so wrappers like mpicxx automatically include flags like
"-Wp,-D_GLIBCXX_ASSERTIONS", which in this case causes opal to fail to run,
because of an assertion failure in stl_vector. I've included the stack
below. I've worked around this by patching mpicxx & company, but I suspect
it might be useful to turn on _GLIBCXX_ASSERTIONS to find some latent bugs
in the code.
Cheers,
Rob
(gdb) run opal.in
Starting program: /home/vagrant/.local/bin/opal opal.in
Missing separate debuginfos, use: dnf debuginfo-install
glibc-2.31-4.fc32.x86_64
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Ippl> CommMPI: Parent process waiting for children ...
Ippl> CommMPI: Initialization complete.
> ____ _____ ___
> / __ \| __ \ /\ | |
> | | | | |__) / \ | |
> | | | | ___/ /\ \ | |
> | |__| | | / ____ \| |____
> \____/|_| /_/ \_\______|
OPAL>
OPAL> This is OPAL (Object Oriented Parallel Accelerator Library) Version
2.4.0
OPAL> git rev. unknown
OPAL>
OPAL>
OPAL> (c) PSI, http://amas.web.psi.ch
OPAL>
OPAL>
OPAL> The optimiser (former opt-Pilot) is integrated
OPAL>
OPAL> Please send cookies, goodies or other motivations (wine and beer ... )
OPAL> to the OPAL developers opal@lists.psi.ch
OPAL>
OPAL> Time: 23:59:38 date: 22/12/2020
OPAL>
OPAL> Couldn't find startup file "/home/vagrant/init.opal".
OPAL> Note: this is not mandatory for an OPAL simulation!
OPAL>
OPAL> * Reading input stream "opal.in".
OPAL> *
**********************************************************************************
OPAL> * Selected Tracking Method == PARALLEL-T, NEW TRACK
OPAL> *
**********************************************************************************
/usr/include/c++/10/bits/stl_vector.h:1045: std::vector<_Tp,
_Alloc>::reference std::vector<_Tp, _Alloc>::operator[](std::vector<_Tp,
_Alloc>::size_type) [with _Tp = char; _Alloc = std::allocator<char>; \
std::vector<_Tp, _Alloc>::reference = char&; std::vector<_Tp,
_Alloc>::size_type = long unsigned int]: Assertion '__builtin_expect(__n <
this->size(), true)' failed.
Program received signal SIGABRT, Aborted.
0x00007ffff683e9e5 in raise () from /lib64/libc.so.6
Missing separate debuginfos, use: dnf debuginfo-install
blas-3.9.0-3.fc32.x86_64 bzip2-libs-1.0.8-2.fc32.x86_64
gsl-2.6-2.fc32.x86_64 hdf5-mpich-1.10.5-6.fc32.x86_64
hwloc-libs-2.0.4-3.fc32.x86_64 lapack\
-3.9.0-3.fc32.x86_64 libaec-1.0.4-3.fc32.x86_64 libgcc-10.2.1-6.fc32.x86_64
libgfortran-10.2.1-6.fc32.x86_64 libicu-65.1-2.fc32.x86_64
libquadmath-10.2.1-6.fc32.x86_64 libstdc++-10.2.1-6.fc32.x86_64 libt\
ool-ltdl-2.4.6-33.fc32.x86_64 mpich-3.3.2-4.fc32.x86_64
xz-libs-5.2.5-1.fc32.x86_64 zlib-1.2.11-21.fc32.x86_64
(gdb) bt
bt
#0 0x00007ffff683e9e5 in raise () from /lib64/libc.so.6
#1 0x00007ffff6827895 in abort () from /lib64/libc.so.6
#2 0x0000555555e9cb38 in std::__replacement_assert
(__file=__file@entry=0x5555578604d0
"/usr/include/c++/10/bits/stl_vector.h", __line=__line@entry=1045,
__function=__function@entry=0x555557880338 "std::vector<_Tp,
_Alloc>::reference std::vector<_Tp, _Alloc>::operator[](std::vector<_Tp,
_Alloc>::size_type) [with _Tp = char; _Alloc = std::allocator<cha\
r>; std::vector<_Tp, _Alloc>::reference = cha"...,
__condition=__condition@entry=0x555557860370 "__builtin_expect(__n <
this->size(), true)")
at /usr/include/c++/10/x86_64-redhat-linux/bits/c++config.h:2560
#3 0x0000555556329045 in std::vector<char, std::allocator<char>
>::operator[] (__n=0, this=0x7fffffffb750) at
/usr/include/c++/10/bits/ios_base.h:170
#4 Distribution::createDistributionFromFile (this=0x5555585afe50,
massIneV=<optimized out>) at
/home/vagrant/src-OPAL-2.4.0/src/Distribution/Distribution.cpp:1109
#5 0x00005555563295f0 in Distribution::create (this=0x5555585afe50,
numberOfParticles=@0x555558616c70: 10000, massIneV=510998.95000000001,
charge=-1)
at /home/vagrant/src-OPAL-2.4.0/src/Distribution/Distribution.cpp:290
#6 0x000055555632a015 in Distribution::createOpalT (this=0x5555585afe50,
beam=0x5555585b3bb0, numberOfParticles=@0x7fffffffc228: 10000) at
/usr/include/c++/10/bits/stl_vector.h:1092
#7 0x00005555560a403c in PartBunchBase<double, 3u>::setDistribution
(np=@0x7fffffffc228: 10000, addedDistributions=..., d=<optimized out>,
this=0x5555585b3bb0)
at /usr/include/c++/10/bits/stl_algobase.h:560
#8 TrackRun::setDistributionParallelT (this=0x5555585b5ba0,
beam=0x5555585af8d0) at
/home/vagrant/src-OPAL-2.4.0/src/Track/TrackRun.cpp:680
#9 0x00005555560a9282 in TrackRun::setupTTracker (this=0x5555585b5ba0) at
/home/vagrant/src-OPAL-2.4.0/src/Track/TrackRun.cpp:353
#10 0x00005555560aa482 in TrackRun::execute (this=0x5555585b5ba0) at
/home/vagrant/src-OPAL-2.4.0/src/Track/TrackRun.cpp:174
#11 0x0000555555f3a46f in OpalParser::execute (this=<optimized out>,
object=0x5555585b5ba0, name="RUN") at
/home/vagrant/src-OPAL-2.4.0/src/OpalParser/OpalParser.cpp:139
#12 0x0000555555f3e054 in OpalParser::parseAction (this=0x5555585b2870,
stat=...) at /home/vagrant/src-OPAL-2.4.0/src/OpalParser/OpalParser.cpp:172
#13 0x0000555555f3e6a4 in OpalParser::parse (this=0x5555585b2870, stat=...)
at /home/vagrant/src-OPAL-2.4.0/src/OpalParser/OpalParser.cpp:90
#14 0x0000555555f3e42e in OpalParser::run (this=0x5555585b2870) at
/home/vagrant/src-OPAL-2.4.0/src/OpalParser/OpalParser.cpp:607
#15 0x00005555560a25b0 in TrackCmd::execute (this=<optimized out>) at
/home/vagrant/src-OPAL-2.4.0/src/Track/TrackCmd.cpp:211
#16 0x0000555555f3a46f in OpalParser::execute (this=<optimized out>,
object=0x5555585b2050, name="TRACK") at
/home/vagrant/src-OPAL-2.4.0/src/OpalParser/OpalParser.cpp:139
#17 0x0000555555f3b3b0 in OpalParser::parseDefine (this=0x7fffffffd850,
stat=...) at /home/vagrant/src-OPAL-2.4.0/src/OpalParser/OpalParser.cpp:356
#18 0x0000555555f3e65c in OpalParser::parse (this=0x7fffffffd850, stat=...)
at /home/vagrant/src-OPAL-2.4.0/src/OpalParser/OpalParser.cpp:82
#19 0x0000555555f3e42e in OpalParser::run (this=0x7fffffffd850) at
/home/vagrant/src-OPAL-2.4.0/src/OpalParser/OpalParser.cpp:607
#20 0x0000555555f3a9f8 in OpalParser::run (this=0x7fffffffd850,
is=<optimized out>) at
/home/vagrant/src-OPAL-2.4.0/src/OpalParser/OpalParser.cpp:632
#21 0x0000555555e6e4b7 in main (argc=<optimized out>, argv=<optimized out>)
at /home/vagrant/src-OPAL-2.4.0/src/Main.cpp:349
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~OPAL 2021.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/626Add RING cyclotron fieldmap type2020-12-10T09:23:33+01:00ext-calvo_ppedro.calvo@ciemat.esAdd RING cyclotron fieldmap type`RING` fieldmap type (PSI format measured field file) for cyclotron is considered as default if one of the other types are not mentioned. I propose to add this `TYPE` explicitly to the different options, to prevent the bad assignment of ...`RING` fieldmap type (PSI format measured field file) for cyclotron is considered as default if one of the other types are not mentioned. I propose to add this `TYPE` explicitly to the different options, to prevent the bad assignment of the `TYPE` parameter.OPAL 2021.1ext-calvo_ppedro.calvo@ciemat.esext-calvo_ppedro.calvo@ciemat.eshttps://gitlab.psi.ch/OPAL/src/-/issues/624PyOpal - build system2022-09-14T11:43:03+02:00ext-rogers_cPyOpal - build system### Summary
Build system and a couple of simple examples for opal<->python API
I would like to merge in my current working tree, by way of debugging all of the build system stuff for pyopal. At the moment I have working code that will ...### Summary
Build system and a couple of simple examples for opal<->python API
I would like to merge in my current working tree, by way of debugging all of the build system stuff for pyopal. At the moment I have working code that will allow users to link against python and build C/python libraries. I have implemented a couple of examples:
* Access to a few polynomial routines
* Access to the OpalRing for field lookups
Obviously not full implementation of #516 but an opportunity to get a bit of feedback on the interface for building libraries/etc.
~"Feature request"2022.1ext-rogers_cext-rogers_chttps://gitlab.psi.ch/OPAL/src/-/issues/622Check read of FROMFILE distribution2020-12-01T09:03:37+01:00ext-calvo_ppedro.calvo@ciemat.esCheck read of FROMFILE distributionThere is an `OpalException` in `Distribution::createDistributionFromFile` to check if the external file of the initial distribution exists. But it is not working in parallel environment.There is an `OpalException` in `Distribution::createDistributionFromFile` to check if the external file of the initial distribution exists. But it is not working in parallel environment.OPAL 2021.1ext-calvo_ppedro.calvo@ciemat.esext-calvo_ppedro.calvo@ciemat.eshttps://gitlab.psi.ch/OPAL/src/-/issues/621DerivePointerAlignment must be set to false in .clang-format2020-11-26T10:51:25+01:00gsellDerivePointerAlignment must be set to false in .clang-formatAs noticed in !361 the DerivePointerAlignment should be set to false.As noticed in !361 the DerivePointerAlignment should be set to false.OPAL 2021.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/620Header of loss files2020-11-30T16:49:59+01:00ext-calvo_ppedro.calvo@ciemat.esHeader of loss files### Summary
Bad implementation of the header in ASCII files
### What is the current *bug* behavior?
The header of loss files in ASCII format is bad written when simulations are performed in parallel environment and the time variable ...### Summary
Bad implementation of the header in ASCII files
### What is the current *bug* behavior?
The header of loss files in ASCII format is bad written when simulations are performed in parallel environment and the time variable is considered. If the node 0 has no particles, the header is incomplete
### What is the expected *correct* behavior?
The header should include `turn`, `bunchNum` and `time` variables
### Possible fixes
Make use of `hasTimeAttribute()` functionOPAL 2021.1ext-calvo_ppedro.calvo@ciemat.esext-calvo_ppedro.calvo@ciemat.eshttps://gitlab.psi.ch/OPAL/src/-/issues/618replace uint with unsigned int2020-11-06T08:53:14+01:00gsellreplace uint with unsigned int`uint` is not a standardised type in C++. It should be replaced with `unsigned int`.
On macOS compilation is failing with current Xcode with the error
```
error: 'uint' was not declared in this scope
````uint` is not a standardised type in C++. It should be replaced with `unsigned int`.
On macOS compilation is failing with current Xcode with the error
```
error: 'uint' was not declared in this scope
```OPAL 2021.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/617add clang-format configuration file2020-10-14T12:59:24+02:00gselladd clang-format configuration fileIn the discussion on the opal-developers mailing list about the code formatting tool there was a - not ver strong - preference to use clang-format, mainly due to it simpler configuration.
clang-format is able to support our coding-style...In the discussion on the opal-developers mailing list about the code formatting tool there was a - not ver strong - preference to use clang-format, mainly due to it simpler configuration.
clang-format is able to support our coding-style. Nevertheless in some cases reformatting is a bit ugly. In the worst-case reformatting can easily be disabled for some lines of code by enclosing them in `// clang-format off` add `// clang-format on`.OPAL 2021.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/615Opal version in master branch2020-10-09T13:30:32+02:00ext-calvo_ppedro.calvo@ciemat.esOpal version in master branchOPAL VERSION should be change to 2.5 in master branch (CMakeLists.txt actually shows 2.3)OPAL VERSION should be change to 2.5 in master branch (CMakeLists.txt actually shows 2.3)ext-calvo_ppedro.calvo@ciemat.esext-calvo_ppedro.calvo@ciemat.es