Merge branch 'develop' into develop

SmileiPIC · Dec 6, 2023 · 15b43ae · 15b43ae
2 parents a13e6d2 + 02a7520
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diff --git a/doc/Sphinx/Overview/material.rst b/doc/Sphinx/Overview/material.rst
@@ -47,6 +47,49 @@ As of November 2021, 90 papers have been published covering a broad range of top
    There is now a utility to add new entries to this list.
    Use the python script doc/doi2publications.py to generate entries from a DOI number, and paste them here
 
+
+.. [Guo2023]
+
+    A. Guo, Q. Lu, S. Lu, S. Wang and R. Wang,
+    `Properties of Electron-scale Magnetic Reconnection at a Quasi-perpendicular Shock`,
+    `The Astrophysical Journal 955, 1 (2023) <https://doi.org/10.3847/1538-4357/acec48>`_
+       
+.. [Si2023]
+
+    M. Si, Y. Huang, M. Ruan, B. Shen, Z. Xu, T. Yu, X. Wang and Y. Chen,
+    `Relativistic-guided stable mode of few-cycle 20 micron level infrared radiation`,
+    `Optics Express 31, 24, 40202-40209 (2023) <https://doi.org/10.1364/OE.503814>`_
+       
+.. [Vallieres2023]
+
+    S. Vallières, J. Powell, T. Connell, M. Evans, M. Lytova, F. Fillion-Gourdeau, S. Fourmaux, S. Payeur, P. Lassonde, S. MacLean, and F. Légaré,
+    `High Dose-Rate MeV Electron Beam from a Tightly-Focused Femtosecond IR Laser in Ambient Air`,
+    `Laser and Photonics Review 23000782300078 (2023) <https://doi.org/10.1002/lpor.202300078>`_
+
+.. [Starodubtseva2023]
+
+    E. Starodubtseva, I. Tsymbalov, D. Gorlova, K. Ivanov, and A. Savel'ev,
+    `Low energy electron injection for direct laser acceleration`,
+    `Phys. Plasmas 30, 083105 (2023) <https://doi.org/10.1063/5.0155196>`_
+
+.. [Maffini2023]
+
+    A. Maffini, F. Mirani, M. Galbiati, K. Ambrogioni, F. Gatti, M. S. G. De Magistris, D. Vavassori, D. Orecchia, D. Dellasega, V. Russo, M. Zavelani-Rossi and M. Passoni,
+    `Towards compact laser-driven accelerators: exploring the potential of advanced double-layer targets`,
+    `EPJ Techniques and Instrumentation 10, 15 (2023) <https://doi.org/10.1140/epjti/s40485-023-00102-8>`_
+       
+.. [Guskov2023]
+
+    S. Yu. Gus'kov, Ph. Korneev, and M. Murakami,
+    `Laser-driven electrodynamic implosion of fast ions in a thin shell`,
+    `Matter Radiat. Extremes 8, 056602 (2023) <https://doi.org/10.1063/5.0156113>`_
+
+.. [RezaeiPandari2023]
+
+    M. Rezaei-Pandari, M. Mirzaie, C. I. Hojbota, T. G. Pak, S. B. Kim, G. W. Lee, R. Massudi, A. R. Niknam, S. K. Lee, K.-Y. Kim, and C. H. Nam,
+    `Laser Wakefield Electron Acceleration with Polarization-Dependent Ionization Injection`,
+    `Physical Review Applied 20, 034026 (2023) <http://dx.doi.org/10.1103/PhysRevApplied.20.034026>`_
+    
 .. [Jonnerby2023]
 
       J. Jonnerby, A. von Boetticher, J. Holloway, L. Corner, A. Picksley, A. J. Ross, R. J. Shalloo , C. Thornton, N. Bourgeois, R. Walczak, and S. M. Hooker,
@@ -173,6 +216,25 @@ As of November 2021, 90 papers have been published covering a broad range of top
     `Electron acceleration by laser plasma wedge interaction`,
     `Phys. Rev. Research 5, 013115 (2023) <http://dx.doi.org/10.1103/PhysRevResearch.5.013115>`_
 
+.. [Bukharskii2022]
+
+    N. Bukharskii, Iu. Kochetkov and Ph. Korneev,
+    `Terahertz annular antenna driven with a short intense laser pulse`,
+    `Applied Physics Letters 120, 014102 (2022) <https://doi.org/10.1063/5.0076700>`_
+            
+
+.. [Jirka2022]
+
+    M. Jirka, P. Sasorov and S. V. Bulanov,
+    `New and old physics in the interaction of a radiating electron with the extreme electromagnetic field`,
+    `Physical Review D 105, 113004 (2022) <https://doi.org/10.1103/PhysRevD.105.113004>`_
+        
+.. [Geng2022]
+
+    X. Geng, L. Ji and B. Shen,
+    `Quasimonochromatic Bright Gamma-ray Generation from Synchronized Compton Scattering via Azimuthal Spatial-Temporal Coupling`,
+    `Physical Review Applied 17, 024055 (2022) <https://doi.org/10.1063/5.0084870>`_
+              
 .. [Yan2022]
 
     X. Yan, Y. Wu, X. Geng, H. Zhang, B. Shen and L. Ji,
@@ -306,8 +368,6 @@ As of November 2021, 90 papers have been published covering a broad range of top
   `Stimulated-Raman-scattering amplification of attosecond XUV pulses with pulse-train pumps and application to local in-depth plasma-density measurement`,
   `Phys. Rev. E 106, 045208 (2022) <http://dx.doi.org/10.1103/PhysRevE.106.045208>`_
 
-
-
 .. [Krafft2022b]
 
   C. Krafft and P. Savoini,
@@ -369,7 +429,18 @@ As of November 2021, 90 papers have been published covering a broad range of top
   `In International Conference on High Performance Computing in Asia-Pacific Region Workshops (HPCAsia 2022 Workshop). 
   Association for Computing Machinery, New York, NY, USA, 40–48. (2022) <http://doi.org/10.1145/3503470.3503475>`_
 
+.. [Tiwary2021]
 
+  S. Tiwary and N. Kumar,
+  `Particle jets in colliding two ultraintense laser pulses of varying frequencies`,
+  `Physical Review Research 3, 043190 (2021) <https://doi.org/10.1103/PhysRevResearch.3.043190>`_
+
+.. [Spiers2021]
+
+  B. T. Spiers, R. Aboushelbaya, Q. Feng, M. W. Mayr, I. Ouatu, R. W. Paddock, R. Timmis, R. H.-W. Wang  and P. A. Norreys,
+  `Methods for extremely sparse-angle proton tomography`,
+  `Physical Review E 104, 045201 (2021) <https://doi.org/10.1103/PhysRevE.104.045201>`_
+      
 .. [Tomassini2021]
 
     Paolo Tomassini, Francesco Massimo, Luca Labate and Leonida A. Gizzi,

diff --git a/doc/Sphinx/Overview/releases.rst b/doc/Sphinx/Overview/releases.rst
@@ -29,6 +29,10 @@ Changes made in the repository (not released)
   * Changed coordinate reference for 2D probe in 3D or AM geometry
     (zero is the box origin projected orthogonally on the probe plane).
 
+* Bug fixes:
+
+  * ``dump_minutes`` often failed to write some checkpoint files.
+
 ----
 
 Projects

diff --git a/happi/_Diagnostics/Probe.py b/happi/_Diagnostics/Probe.py
@@ -53,8 +53,9 @@ def _init(self, requestedProbe=None, field=None, timesteps=None, subset=None, av
 		self._dataForTime = {}
 		for file in self._h5probe:
 			for key, val in file.items():
-				try   : self._dataForTime[int(key)] = val
-				except Exception as e: break
+				if val:
+					try   : self._dataForTime[int(key)] = val
+					except Exception as e: break
 		self._alltimesteps = self._np.double(sorted(self._dataForTime.keys()))
 		if self._alltimesteps.size == 0:
 			raise Exception("No timesteps found")

diff --git a/src/Checkpoint/Checkpoint.cpp b/src/Checkpoint/Checkpoint.cpp
@@ -35,6 +35,7 @@
 #include "LaserEnvelope.h"
 #include "BinaryProcesses.h"
 #include "CollisionalNuclearReaction.h"
+#include <unistd.h>
 
 using namespace std;
 
@@ -49,11 +50,9 @@ Checkpoint::Checkpoint( Params &params, SmileiMPI *smpi ) :
     dump_minutes( 0.0 ),
     exit_after_dump( true ),
     time_reference( MPI_Wtime() ),
-    time_dump_step( 0 ),
     keep_n_dumps( 2 ),
     keep_n_dumps_max( 10000 ),
     dump_deflate( 0 ),
-    dump_request( smpi->getSize() ),
     file_grouping( 0 )
 {
 
@@ -66,7 +65,7 @@ Checkpoint::Checkpoint( Params &params, SmileiMPI *smpi ) :
 
         PyTools::extract( "dump_minutes", dump_minutes, "Checkpoints"  );
         if( dump_minutes > 0 ) {
-            MESSAGE( 1, "Code will stop after " << dump_minutes << " minutes" );
+            MESSAGE( 1, "Code will dump after " << dump_minutes << " minutes" );
         }
 
         PyTools::extract( "keep_n_dumps", keep_n_dumps, "Checkpoints"  );
@@ -186,40 +185,27 @@ Checkpoint::~Checkpoint() {}
 
 void Checkpoint::dump( VectorPatch &vecPatches, Region &region, unsigned int itime, SmileiMPI *smpi, SimWindow *simWindow, Params &params )
 {
-
-    // check for excedeed time
-    if( dump_minutes != 0.0 ) {
-        int tagUB = smpi->getTagUB();
+    bool dump_now = false;
+
+    // Find out whether we should make a checkpoint due to dump_minutes
+    if( dump_minutes != 0. ) {
         // master checks whenever we passed the time limit
-        if( smpi->isMaster() && time_dump_step==0 ) {
-            double elapsed_time = ( MPI_Wtime() - time_reference )/60.;
-            if( elapsed_time > dump_minutes ) {
-                time_dump_step = itime+1; // we will dump at next timestep (in case non-master already passed)
-                MESSAGE( "Reached time limit : " << elapsed_time << " minutes. Dump timestep : " << time_dump_step );
-                // master does a non-blocking send
-                for( unsigned int dest=0; dest < ( unsigned int ) smpi->getSize(); dest++ ) {
-                    MPI_Isend( &time_dump_step, 1, MPI_UNSIGNED, dest, tagUB, smpi->world(), &dump_request[dest] );
-                }
-            }
-        } else { // non master nodes receive the time_dump_step (non-blocking)
-            int todump=0;
-            MPI_Iprobe( 0, tagUB, MPI_COMM_WORLD, &todump, &dump_status_prob );
-            if( todump ) {
-                MPI_Recv( &time_dump_step, 1, MPI_UNSIGNED, 0, tagUB, smpi->world(), &dump_status_recv );
-            }
+        if( smpi->isMaster() &&  MPI_Wtime() - time_reference > dump_minutes * 60. ) {
+            dump_now = true;
         }
-        smpi->barrier();
+        // Broadcast the result
+        MPI_Bcast( &dump_now, 1, MPI_CXX_BOOL, 0, smpi->world() );
     }
-
-    if( signal_received!=0 ||
-            ( dump_step != 0 && ( ( itime-this_run_start_step ) % dump_step == 0 ) ) ||
-            ( time_dump_step!=0 && itime==time_dump_step ) ) {
+
+    // Dump if at requested timestep
+    dump_now = dump_now || ( dump_step != 0 && ( ( itime-this_run_start_step ) % dump_step == 0 ) );
+
+    if( signal_received != 0 || dump_now ) {
         dumpAll( vecPatches, region, itime,  smpi, simWindow, params );
         if( exit_after_dump || ( ( signal_received!=0 ) && ( signal_received != SIGUSR2 ) ) ) {
-            exit_asap=true;
+            exit_asap = true;
         }
-        signal_received=0;
-        time_dump_step=0;
+        signal_received = 0;
         time_reference = MPI_Wtime();
     }
 }

diff --git a/src/Checkpoint/Checkpoint.h b/src/Checkpoint/Checkpoint.h
@@ -63,9 +63,6 @@ class Checkpoint
     //! incremental number of times we've done a dump
     unsigned int dump_number;
 
-    //! incremental number of times we've done a dump_minutes
-    unsigned int dump_minutes_times;
-
     //! this static variable is defined (in the .cpp) as false but becomes true when
     //! the signal SIGUSR1 is captured by the signal_callback_handler fnction
     static int signal_received;
@@ -113,19 +110,13 @@ class Checkpoint
     void dumpMovingWindow( H5Write &f, SimWindow *simWindow );
     void restartMovingWindow( H5Read &f, SimWindow *simWindow );
 
-    //! function that returns elapsed time from creator (uses private var time_reference)
-    //double time_seconds();
-
     //! to dump and stop a simulation you might just check if a file named stop has been created this variable
     //! is true if since last time a file named stop appeared
     bool stop_file_seen_since_last_check;
 
-    //! time of the constructor
+    //! Last dump time
     double time_reference;
 
-    //! step at which perform a dump in case time_dump returns true
-    unsigned int time_dump_step;
-
     //! keep the last keep_n_dumps dump files
     unsigned int keep_n_dumps;
     const unsigned int keep_n_dumps_max;
@@ -136,10 +127,6 @@ class Checkpoint
     //! int deflate dump value
     int dump_deflate;
 
-    std::vector<MPI_Request> dump_request;
-    MPI_Status dump_status_prob;
-    MPI_Status dump_status_recv;
-
     //! group checkpoint files in subdirs of file_grouping files
     unsigned int file_grouping;