handle reading from zero size datasets properly

python/loadleveller/clusterutils.py

@@ -4,12 +4,11 @@ import sys
 
 batchscript_claix18 = '''#!/usr/bin/env zsh
 
-# Autogenerated by loadleveller targeting the claix18 cluster. Do not edit.
+# Autogenerated jobscript targeting the claix18 cluster.
 
 #SBATCH --job-name={jobname}
 #SBATCH --time={walltime}
 #SBATCH --mem-per-cpu={mem_per_cpu}
-##SBATCH --account={project} #TODO
 #SBATCH --ntasks={num_cores}
 #SBATCH --export=NONE
 #SBATCH --output=output.%x
@@ -19,32 +18,38 @@ batchscript_claix18 = '''#!/usr/bin/env zsh
 {mpirun} $FLAGS_MPI_BATCH {mc_cmd}
 '''
 
-batchscript_templates = {
-    'claix18': batchscript_claix18
-}
-
 batch_commands = {
     'claix18': 'sbatch {batchscript}'
 }
 
 valid_systems = ['local', 'claix18']
 
-def generate_batchscript(template, cmd, jobname, jobconfig):
+def generate_batchscript_claix18(cmd, jobname, jobconfig):
+    template = batchscript_claix18
+
+    custom_cmds = ''
+    if 'project' in jobconfig:
+        custom_cmds += '#SBATCH --account={}\n'.format(jobconfig['project'])
+    custom_cmds += jobconfig.get('custom_cmds', '')
+
     try:
         return template.format(
             jobname=jobname,
             mpirun=jobconfig.get('mpirun','mpirun'),
             mem_per_cpu=jobconfig.get('mem_per_cpu','2G'),
             walltime=jobconfig['mc_walltime'],
-            project=jobconfig.get('project',''),
             num_cores=jobconfig['num_cores'],
-            custom_cmds=jobconfig.get('custom_cmds',''),
+            custom_cmds=custom_cmds,
             mc_cmd=' '.join(cmd)
         )
     except KeyError as e:
-        print('Error: required key "{}" missing in jobconfig'.format(e.args[0]))
-        sys.exit(1)
+        raise Exception('Error: required key "{}" missing in jobconfig'.format(e.args[0]))
         
+def generate_batchscript(sysinfo, *args):
+    if sysinfo == 'claix18':
+        return generate_batchscript_claix18(*args)
+    else:
+        raise Exception('unknown system type {}'.format(sysinfo))
 
 def determine_system():
     sysinfo = os.environ.get('MCLL_SYSTEM_INFO')
@@ -71,7 +76,7 @@ def run(jobname, jobconfig, cmd):
         os.system(mpicmd)
     else:
         with tempfile.NamedTemporaryFile(mode='w',delete=False) as f:
-            batchscript = generate_batchscript(batchscript_templates[sysinfo], cmd, jobname, jobconfig)
+            batchscript = generate_batchscript(sysinfo, cmd, jobname, jobconfig)
             print(batchscript)
             f.write(batchscript)
             bscriptname = f.name

src/dump.cpp

@@ -26,8 +26,8 @@ static herr_t H5Ewalk_cb(unsigned int n, const H5E_error2_t *err_desc, void *cli
 	char *maj_str = H5Eget_major(err_desc->maj_num);
 	s << fmt::format("#{}: {}:{} in {}(): {}\n", n, err_desc->file_name, err_desc->line,
 	                 err_desc->func_name, err_desc->desc);
-	s << fmt::format("    {}: {}\n", static_cast<int>(err_desc->maj_num), maj_str);
-	s << fmt::format("    {}: {}\n\n", static_cast<int>(err_desc->min_num), min_str);
+	s << fmt::format("    {}: {}\n", static_cast<int32_t>(err_desc->maj_num), maj_str);
+	s << fmt::format("    {}: {}\n\n", static_cast<int32_t>(err_desc->min_num), min_str);
 
 	free(min_str);
 	free(maj_str);

src/dump.h

@@ -240,6 +240,10 @@ void iodump::group::read(const std::string &name, std::vector<T> &data) const {
 		throw iodump_exception{"H5Sget_simple_extent_npoints"};
 	data.resize(size);
 
+	if(size == 0) { // handle empty dataset correctly
+		return;
+	}
+
 	herr_t status =
 	    H5Dread(*dataset, h5_datatype<T>(), H5S_ALL, H5P_DEFAULT, H5P_DEFAULT, data.data());
 	if(status < 0)