src issueshttps://gitlab.psi.ch/OPAL/src/-/issues2018-03-30T19:06:21+02:00https://gitlab.psi.ch/OPAL/src/-/issues/202Scan-1 regression test is broken2018-03-30T19:06:21+02:00snuverink_jjochem.snuverink@psi.chScan-1 regression test is brokenNow that the Scan option is fixed (issue #2) the regression test [Scan-1](https://gitlab.psi.ch/OPAL/regression-tests/tree/master/RegressionTests/Scan-1) looks [better](http://amas.web.psi.ch/opal/regressionTests/master/results_2018-01-0...Now that the Scan option is fixed (issue #2) the regression test [Scan-1](https://gitlab.psi.ch/OPAL/regression-tests/tree/master/RegressionTests/Scan-1) looks [better](http://amas.web.psi.ch/opal/regressionTests/master/results_2018-01-08.xml#Scan-1_rms_x), but is still broken.
@kraus: do you perhaps understand why?OPAL 2.0.0snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/src/-/issues/214Typo in CMakeLists.txt, line 532018-03-22T16:33:27+01:00ext-neveu_nTypo in CMakeLists.txt, line 53Line 53: ` add_comile_options (-diag-disable 383 -diag-disable 981)`
There's a missing 'p' in compile on this line.Line 53: ` add_comile_options (-diag-disable 383 -diag-disable 981)`
There's a missing 'p' in compile on this line.https://gitlab.psi.ch/OPAL/src/-/issues/208Destructors are noexcept(true) in C++112018-03-22T16:33:26+01:00frey_mDestructors are noexcept(true) in C++11With ```gcc/7.3.0``` one gets the following warning due to the ```CLOSE_FILE``` macro in ```LossDataSink```:
```
src/Classic/Structure/LossDataSink.cpp: In destructor 'LossDataSink::~LossDataSink()':
/scratch1/scratchdirs/frey_m/libs/op...With ```gcc/7.3.0``` one gets the following warning due to the ```CLOSE_FILE``` macro in ```LossDataSink```:
```
src/Classic/Structure/LossDataSink.cpp: In destructor 'LossDataSink::~LossDataSink()':
/scratch1/scratchdirs/frey_m/libs/opal/src/src/Classic/Structure/LossDataSink.cpp:100:70: warning: throw will always call terminate() [-Wterminate]
throw GeneralClassicException(std::string(__func__), ss.str()); \
^
/scratch1/scratchdirs/frey_m/libs/opal/src/src/Classic/Structure/LossDataSink.cpp:156:9: note: in expansion of macro 'CLOSE_FILE'
CLOSE_FILE ();
^
/scratch1/scratchdirs/frey_m/libs/opal/src/src/Classic/Structure/LossDataSink.cpp:100:70: note: in C++11 destructors default to noexcept
throw GeneralClassicException(std::string(__func__), ss.str()); \
```
As the warning explains: In C++11 destructors are ```noexcept(true)``` by default. I'll fix this by setting the destructor ```noexcept(false)``` explicitly.OPAL 1.9.xfrey_mfrey_mhttps://gitlab.psi.ch/OPAL/src/-/issues/73'RestartTest-2' fails on master branch2018-03-20T10:08:59+01:00gsell'RestartTest-2' fails on master branch'RestartTest-2' fails with the following error message:
```
Error{0}> get_iter(): no more items in Message
Error{0}> reduce: mismatched element count in vector reduction.
```'RestartTest-2' fails with the following error message:
```
Error{0}> get_iter(): no more items in Message
Error{0}> reduce: mismatched element count in vector reduction.
```OPAL 1.9.xadelmannadelmannhttps://gitlab.psi.ch/OPAL/src/-/issues/212Cyclotron example in manual is broken2018-03-19T15:17:59+01:00adelmannCyclotron example in manual is brokenThe example (https://gitlab.psi.ch/OPAL/src/wikis/Cyclotron). in the Wiki manual does not work as pointed out by Kengo-sanThe example (https://gitlab.psi.ch/OPAL/src/wikis/Cyclotron). in the Wiki manual does not work as pointed out by Kengo-sanOPAL 2.0.0snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/src/-/issues/18OPAL-Cyc: Mixing coordinates and momenta for ID02018-03-16T06:03:55+01:00Valeria RizzoglioOPAL-Cyc: Mixing coordinates and momenta for ID0The first two particles from the input beam are:
```
0.000 0.000 0.000 0.0000 0.0000 0.0000
0.000 -0.0074186 0.0000 0.00000 0.0000 0.00000
```
the OFFSETZ and OFFSETY have been used in the input file: OFFSETZ = 0.15 m and OFFSETY =...The first two particles from the input beam are:
```
0.000 0.000 0.000 0.0000 0.0000 0.0000
0.000 -0.0074186 0.0000 0.00000 0.0000 0.00000
```
the OFFSETZ and OFFSETY have been used in the input file: OFFSETZ = 0.15 m and OFFSETY = 0.0001 m
**Outputs**
* **Step 0**
** **Track-orbit**: it is already known that the y and z coordinates for ID0 are not updated with respect to OFFSETY and OFFSETZ. X-coor is correct.
```
x [mm] beta_x*gamma y [mm] beta_y*gamma z [mm] beta_z*gamma
ID0 -1.30000000e+03 -3.30872245e-24 2.71050543e-17 7.41857376e-01 -2.58493941e-26 1.69406589e-21
ID1 -1.30000000e+03 -7.41860000e-03 1.00000000e-01 7.41857376e-01 1.50000000e+02 0.00000000e+00
```
** **H5**: only ID0 coordinates are copied from ID1
```
x [m] y [m] z [m] px py pz
ID0 * -1.3 * 0.0001 * 0.15 * 0 * 0.7418573 * 0 *
ID1 * -1.3 * 0.0001 * 0.15 * -0.007418 * 0.7418573 * 0 *
```
* **Step 100**
** **Track-ordit**
```
x [mm] beta_x*gamma y [mm] beta_y*gamma z [mm] beta_z*gamma
ID0 4.91648494e+02 5.82908115e-01 2.17698321e+03 -2.50847030e-01 2.86192018e+02 3.85769984e-01
ID1 5.14833464e+02 6.81873741e-01 2.19127413e+03 -2.92328139e-01 1.50000000e+02 2.56591691e-16
```
** **H5**
```
x [m] y [m] z [m] px py pz
ID0 * 0.5148334 * 2.1912741 * 0.15 * 0.5829081 * -0.250847 * 0.3857699 *
ID1 * 0.5148334 * 2.1912741 * 0.15 * 0.6818737 * -0.292328 * 0 *
```
* **Conclusions**
1. In case of OFFSETs, the ID0 particle stored in the track-Orbits is not shifted. Depending on the simulation, the track of this particle could be wrong. For example, assuming to place the beam in the mid-plane of a dipole, as in my case, the ID0 particle sees a wrong magnetic field. In my simulation, this particle is useless, it cannot be used as reference particle and removed from the track-Orbit file.
2. In the H5 file, a combination of ID0 and ID1 is stored. The coordinates of ID0 are copied from ID1 (properly tracked in the simulation), while the momenta are from the track of ID0. The result is a mixture of particle coordinates and momenta.
* **Solutions**
1. Update the position of the ID0 (already discussed, but too complicated)
2. Write a note in the manual that explains this situation
3. In the H5 file, copy completely ID1 and not mix two particles.adelmannadelmannhttps://gitlab.psi.ch/OPAL/src/-/issues/205ippl/tests2018-02-09T10:58:07+01:00adelmannippl/testsI need to build IPPL tests for benchmarking purposes.
How do we build these day's?I need to build IPPL tests for benchmarking purposes.
How do we build these day's?krausfrey_mkraushttps://gitlab.psi.ch/OPAL/src/-/issues/19DKS Documentation in OPAL manual2018-01-30T13:42:19+01:00adelmannDKS Documentation in OPAL manualAdd DKS documentation to OPAL manual
- reference to paper
- how to compile
- how to use
- update OPTION, remove DKS
A brief description on how to install cuda and install dks is available on the Wiki. Add DKS documentation to OPAL manual
- reference to paper
- how to compile
- how to use
- update OPTION, remove DKS
A brief description on how to install cuda and install dks is available on the Wiki. OPAL 1.6.0https://gitlab.psi.ch/OPAL/src/-/issues/181timing.dat2018-01-25T12:21:49+01:00adelmanntiming.datAdd problem size to timing.dat
NP == number of particles
MX,MY,MZ == gridsizes
domain decomposition
Not shure how to cover AMR but that is a differnt topic.Add problem size to timing.dat
NP == number of particles
MX,MY,MZ == gridsizes
domain decomposition
Not shure how to cover AMR but that is a differnt topic.https://gitlab.psi.ch/OPAL/src/-/issues/204rename opt-Pilot function sameSDDSVariableAt to statVariableAt2018-01-20T14:15:19+01:00krausrename opt-Pilot function sameSDDSVariableAt to statVariableAtI think the name `sameSDDSVariableAt` isn't a good choice (if I remember correctly it was my own...). This function uses the results of the `.stat` file. Accordingly it should be called `statVariableAt`.I think the name `sameSDDSVariableAt` isn't a good choice (if I remember correctly it was my own...). This function uses the results of the `.stat` file. Accordingly it should be called `statVariableAt`.adelmannkrausadelmannhttps://gitlab.psi.ch/OPAL/src/-/issues/203Structure/H5PartWrapper.cpp Error2018-01-11T08:45:06+01:00adelmannStructure/H5PartWrapper.cpp ErrorOn merlin: */gpfs/home/adelmann/scratch/opal-scaling/Merlin/test* check **scaling-1.o92428**
`Error{91}> H5 rc= -2 in /gpfs/home/adelmann/opal/opal-1.9/src/Structure/H5PartWrapper.cpp @ line 94`
The simulation does not crash maybe als...On merlin: */gpfs/home/adelmann/scratch/opal-scaling/Merlin/test* check **scaling-1.o92428**
`Error{91}> H5 rc= -2 in /gpfs/home/adelmann/opal/opal-1.9/src/Structure/H5PartWrapper.cpp @ line 94`
The simulation does not crash maybe also because **OPTION, PSDUMPFREQ = 1E9;**OPAL 2.0.0krausgsellkraushttps://gitlab.psi.ch/OPAL/src/-/issues/173optimiser run has two times the tmpl file specified2018-01-10T21:15:13+01:00adelmannoptimiser run has two times the tmpl file specifiedargv[1] is a mandatory argument for OPAL, however in case of a optimiser run there is an
additional argument --inputfile=$TEMPLATES/$FNBASE.tmpl. This can be removed and the argv[1] used.argv[1] is a mandatory argument for OPAL, however in case of a optimiser run there is an
additional argument --inputfile=$TEMPLATES/$FNBASE.tmpl. This can be removed and the argv[1] used.OPAL 2.0.0adelmannadelmannhttps://gitlab.psi.ch/OPAL/src/-/issues/183Attributes PC, ENERGY and GAMMA of BEAM command not described2018-01-09T18:53:22+01:00krausAttributes PC, ENERGY and GAMMA of BEAM command not describedThere are several possible definitions for PC
1. $`PC = mc^2 \frac{\sqrt{\sum_i p_{x,i}^2 + p_{y,i}^2 + p_{z,i}^2}}{N}`$
1. $`PC = mc^2 \frac{\sum_i p_{z,i}}{N}`$
Currently the second definition is implemented. This has the advantage th...There are several possible definitions for PC
1. $`PC = mc^2 \frac{\sqrt{\sum_i p_{x,i}^2 + p_{y,i}^2 + p_{z,i}^2}}{N}`$
1. $`PC = mc^2 \frac{\sum_i p_{z,i}}{N}`$
Currently the second definition is implemented. This has the advantage that mean longitudinal momentum is well defined and thereby the reference particle has the same velocity as the centroid. The disadvantage is that the kinematic energy of the bunch is to high.
The definition for PC should be chosen and the two attributes should be described in the manual for 1.6 and 1.9.adelmannsnuverink_jjochem.snuverink@psi.chadelmannhttps://gitlab.psi.ch/OPAL/src/-/issues/2option SCAN broken2018-01-09T09:27:20+01:00adelmannoption SCAN brokenThe option SCAN is broken.The option SCAN is broken.OPAL 1.9.xadelmannadelmannhttps://gitlab.psi.ch/OPAL/src/-/issues/199Rethink catching of exceptions2018-01-09T06:41:26+01:00krausRethink catching of exceptionsCurrently all exceptions are caught by the OpalParser. Whe it catches exceptions then it calls exit. This is a problem for the optimizer since it's very likely that an individual (optimization perspective) failes while the others run smo...Currently all exceptions are caught by the OpalParser. Whe it catches exceptions then it calls exit. This is a problem for the optimizer since it's very likely that an individual (optimization perspective) failes while the others run smoothly.
OpalParser shouldn't catch any exceptions except ParseErrors.krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/14Particles stored in trackOrbit.dat2018-01-05T08:58:48+01:00Valeria RizzoglioParticles stored in trackOrbit.datAccording to the OPAL manual (pag. 40):
**Multi-particle tracking mode**
The intermediate phase space data of centeral particle (with ID of 0) and an off-centering particle (with ID of 1) are stored in an ASCII file.
Concernin...According to the OPAL manual (pag. 40):
**Multi-particle tracking mode**
The intermediate phase space data of centeral particle (with ID of 0) and an off-centering particle (with ID of 1) are stored in an ASCII file.
Concerning the particle with *ID0*:
* particle position is not updated in case OFFSETY > 0 is set in the distribution definition. The tracking of this particle does not reflect the beam behavior (because of the offset)
* Is the general idea: ID0 particle = reference particle?
Concerning the particle with *ID1*:
* ***Distribution from file:*** the second particle in the distribution file is used as ID1
* ***Generated distribution:*** It seems that a random particle from the distribution is set as ID1
A possible suggestion:
* ***Distribution from file:*** the first and the second particle in the file are used as ID0 and ID1, respectively. The user is completely free to decide which particles track.
* ***Generated distribution (Option 1):*** ID0 is by default assigned to the reference particle (with updated offset). An option can be added to the DISTRIBUTION command where the user can specify which particle uses as ID1 (ie: DISPERSION, CENTROID or USERDEF or NULL = not stored). This means that the first two particles generated by OPAL are replaced with ID0 (reference) and ID1, if option NULL is not specified.
* ***Generated distribution (Option 2):*** An option can be added to the DISTRIBUTION command where the user can specify which particle uses as ID0 and ID1 (ie: DISPERSION, CENTROID or USERDEF or or NULL = not stored)
A possible problem could arise in case of multi-distribution or vector of distributionOPAL 1.5.1adelmannadelmannhttps://gitlab.psi.ch/OPAL/src/-/issues/200Optimiser throws unexpected Exceptions and later die2018-01-04T18:14:26+01:00adelmannOptimiser throws unexpected Exceptions and later dieAfter 3ed381f8 I see more Exceptions (merlinl01:/gpfs/home/adelmann/scratch/awa-optim/code/optLinac_40nC.o78706)
I am now a bit more confused:
- the *.data file should only read once (but we have over 600 Exeptions)
- we again have di...After 3ed381f8 I see more Exceptions (merlinl01:/gpfs/home/adelmann/scratch/awa-optim/code/optLinac_40nC.o78706)
I am now a bit more confused:
- the *.data file should only read once (but we have over 600 Exeptions)
- we again have directories that seams to exists
The real problem is reported in merlinl01:/gpfs/home/adelmann/scratch/awa-optim-0/code/optLinac_40nC.o78651
**░░░░░terminate called after throwing an instance of 'OpalException**OPAL 2.0.0krausadelmannYves Ineichenkraushttps://gitlab.psi.ch/OPAL/src/-/issues/178H5root in the binary Linux distribution2017-12-28T14:30:38+01:00adelmannH5root in the binary Linux distribution`
[aandreas@beboplogin1 OPAL-1.6.1]$ source etc/profile.d/opal.sh
[aandreas@beboplogin1 OPAL-1.6.1]$ opal
`
OPAL works as expected.
`
[aandreas@beboplogin1 OPAL-1.6.1]$ H5root
/home/aandreas/OPAL-1.6.1/bin/H5root: line 13: /opt/psi/C...`
[aandreas@beboplogin1 OPAL-1.6.1]$ source etc/profile.d/opal.sh
[aandreas@beboplogin1 OPAL-1.6.1]$ opal
`
OPAL works as expected.
`
[aandreas@beboplogin1 OPAL-1.6.1]$ H5root
/home/aandreas/OPAL-1.6.1/bin/H5root: line 13: /opt/psi/Compiler/H5root/1.3.4/gcc/5.4.0/bin/H5root.bin: No such file or directory
`OPAL 1.6.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/141Improve PAssert to print more diagnostics analog to ASSERT_EQ, ASSERT_LT aso ...2017-12-26T21:58:40+01:00krausImprove PAssert to print more diagnostics analog to ASSERT_EQ, ASSERT_LT aso from GTestASSERT_LT in GTest prints
~/gitwork/opal/ippl/src/Particle/ParticleAttrib.hpp:104: Failure
Expected: (I + M) < (LocalSize), actual: 5039 vs 5039ASSERT_LT in GTest prints
~/gitwork/opal/ippl/src/Particle/ParticleAttrib.hpp:104: Failure
Expected: (I + M) < (LocalSize), actual: 5039 vs 5039krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/197Scan-1 regression test is broken2017-12-21T12:07:54+01:00snuverink_jjochem.snuverink@psi.chScan-1 regression test is brokenThe [Scan-1 regression test](https://gitlab.psi.ch/OPAL/regression-tests/tree/master/RegressionTests/Scan-1) is broken since the beginning of the year.
It seems there were no significant changes to the test.
One thing I don't understan...The [Scan-1 regression test](https://gitlab.psi.ch/OPAL/regression-tests/tree/master/RegressionTests/Scan-1) is broken since the beginning of the year.
It seems there were no significant changes to the test.
One thing I don't understand is why in master the simulation starts at a later s-position, s=0.15m instead of the reference of s=0.0m.
The regression plots show it best:
http://amas.web.psi.ch/opal/regressionTests/master/results_2017-12-19.xml#Scan-1_rms_x