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Fixing memory leaks

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This commit is contained in:
Mark Berrill 2022-07-13 11:20:53 -04:00
parent ed8f5684fd
commit 3cc12ac36e
3 changed files with 202 additions and 27 deletions
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1
CMakeLists.txt
View File

@ -175,5 +175,6 @@ IF ( NOT ONLY_BUILD_DOCS )
ADD_SUBDIRECTORY( example )
#ADD_SUBDIRECTORY( workflows )
INSTALL_PROJ_LIB()
CONFIGURE_FILE( ${CMAKE_CURRENT_SOURCE_DIR}/ValgrindSuppresionFile ${CMAKE_CURRENT_BINARY_DIR}/test/ValgrindSuppresionFile COPYONLY )
ENDIF()

227
ValgrindSuppresionFile
View File

@ -1,52 +1,225 @@
# ACML suppressions
# To run valgrind:
# mpirun -np 2 valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --verbose --suppressions=ValgrindSuppresionFile --log-file=valgrind-out.txt ./lbpm_nernst_planck_cell_simulator test.db
# MPI supressions
{
IdentifyCPUCond
MPI_init_cond
Memcheck:Cond
...
fun:acmlcpuid2
fun:PMPI_Init
...
}
{
IdentifyCPUValue
MPI_init_value
Memcheck:Value8
...
fun:acmlcpuid_once
fun:acmlcpuid2
fun:PMPI_Init
...
}
# MPI suppressions
{
HYD_pmci_wait_for_completion
Memcheck:Leak
...
fun:HYD_pmci_wait_for_completion
fun:main
}
{
HYDT_dmxu_poll_wait_for_event
Memcheck:Leak
...
fun:HYDT_dmxu_poll_wait_for_event
fun:main
}
{
PMPI_Init
Memcheck:Leak
MPI_init_addr16
Memcheck:Addr16
...
fun:PMPI_Init
fun:main
...
}
{
MPI_init_addr8
Memcheck:Addr8
...
fun:PMPI_Init
...
}
{
MPI_init_addr4
Memcheck:Addr4
...
fun:PMPI_Init
...
}
{
MPI_init_addr1
Memcheck:Addr1
...
fun:PMPI_Init
...
}
{
gethostname_cond
Memcheck:Cond
...
fun:gethostbyname_r
fun:gethostbyname
...
}
{
gethostname_value
Memcheck:Value8
...
fun:gethostbyname_r
fun:gethostbyname
...
}
# System suppressions
# System errors
{
map_doit_memory
Memcheck:Cond
fun:index
fun:expand_dynamic_string_token
fun:_dl_map_object
fun:map_doit
fun:_dl_catch_error
...
}
{
expand_dynamic_string_token
Memcheck:Cond
fun:index
fun:expand_dynamic_string_token
...
fun:dl_main
fun:_dl_sysdep_start
fun:_dl_start
...
}
{
call_init
Memcheck:Leak
match-leak-kinds: reachable
...
fun:call_init
fun:_dl_init
...
}
# pthread errors
{
pthread_initialize_param
Memcheck:Param
set_robust_list(head)
fun:__pthread_initialize_minimal
fun:(below main)
}
{
pthread_initialize_cond
Memcheck:Cond
fun:__register_atfork
fun:__libc_pthread_init
fun:__pthread_initialize_minimal
fun:(below main)
}
# gfortran
{
gfortran_leak
Memcheck:Leak
match-leak-kinds: reachable
fun:malloc
obj:/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
...
}
# std
{
libc_cond
Memcheck:Cond
...
fun:_dl_init_paths
fun:_dl_non_dynamic_init
fun:__libc_init_first
fun:(below main)
}
{
libc_val8
Memcheck:Value8
...
fun:_dl_init_paths
fun:_dl_non_dynamic_init
fun:__libc_init_first
fun:(below main)
}
{
mallinfo_cond
Memcheck:Cond
fun:int_mallinfo
fun:mallinfo
...
}
{
mallinfo_value
Memcheck:Value8
fun:int_mallinfo
fun:mallinfo
...
}
{
int_free_cond
Memcheck:Cond
fun:_int_free
...
}
{
string_len_cond
Memcheck:Cond
fun:strlen
...
}
{
int_malloc_cond
Memcheck:Cond
fun:_int_malloc
fun:malloc
...
}
{
malloc_consolidate_malloc
Memcheck:Cond
fun:malloc_consolidate
fun:_int_malloc
...
}
{
malloc_consolidate_free
Memcheck:Cond
fun:malloc_consolidate
fun:_int_free
...
}
{
catch_cond
Memcheck:Cond
fun:__cxa_begin_catch
...
}
{
popen
Memcheck:Param
set_robust_list(head)
fun:__nptl_set_robust
fun:__libc_fork
fun:_IO_proc_open
fun:popen
...
}
{
exit
Memcheck:Value8
fun:__run_exit_handlers
...
fun:exit
...
}
{
sse42
Memcheck:Cond
fun:__strstr_sse42
...
}

1
common/Domain.cpp
View File

@ -87,6 +87,7 @@ void Domain::read_swc(const std::string &Filename) {
List_parent[count] = int(strtod(line2, &line2));
count++;
}
fclose( fid );
cout << " Number of lines extracted is: " << count << endl;
INSIST(count == number_of_lines, "Problem reading swc file!");