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Embed nrnunits.lib #3471

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2ba5043
Embed nrnunits
JCGoran Jun 4, 2025
9cbcb54
Add test
JCGoran Jun 4, 2025
9e0961a
@@@@@@
JCGoran Jun 4, 2025
496a655
Workaround for cpp_cc_build_time_copy
JCGoran Jun 4, 2025
290387a
Sanitizer shenanigans
JCGoran Jun 4, 2025
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13 changes: 11 additions & 2 deletions cmake/ConfigFileSetting.cmake
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Original file line number Diff line number Diff line change
Expand Up @@ -164,8 +164,17 @@ configure_file("${PROJECT_SOURCE_DIR}/src/sundials/sundials_config.h.in"
"${PROJECT_BINARY_DIR}/src/sundials/sundials_config.h" @ONLY)
configure_file("${PROJECT_SOURCE_DIR}/share/lib/nrn.defaults.in"
"${PROJECT_BINARY_DIR}/share/nrn/lib/nrn.defaults" @ONLY)
file(COPY ${PROJECT_SOURCE_DIR}/share/lib/nrnunits.lib
DESTINATION ${PROJECT_BINARY_DIR}/share/nrn/lib)
set(nrnunits_start "")
set(nrnunits_stop "")

configure_file(${PROJECT_SOURCE_DIR}/share/lib/nrnunits.lib.in
${PROJECT_BINARY_DIR}/share/nrn/lib/nrnunits.lib @ONLY)

set(nrnunits_start "R\"qwerty(")
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@nrnhines nrnhines Jun 5, 2025 •
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Optional...Could use a comment. Took me a while (and looking at the constructed embedded_nrnunit.lib file) to realize the reason for the start/stop idiom. I'd never seen this C++ feature before

set(nrnunits_stop ")qwerty\"")
# Embed nrnunits
configure_file(${PROJECT_SOURCE_DIR}/share/lib/nrnunits.lib.in
${PROJECT_BINARY_DIR}/share/nrn/lib/embedded_nrnunits.lib @ONLY)

if(NRN_MACOS_BUILD)
set(abs_top_builddir ${PROJECT_BINARY_DIR})
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4 changes: 2 additions & 2 deletions share/lib/nrnunits.lib → share/lib/nrnunits.lib.in
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This was renamed because we use cpp_cc_build_time_copy on some of the directories, so nrnunits.lib was first set-up at configure time, but then cpp_cc_build_time_copy would clobber it at build-time, so to work around it, we just rename it.

Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
/ from gnu units distribution
@nrnunits_start@/ from gnu units distribution
/ Nov, 2017 updated faraday, R, e, planck, hbar, mole, k according to
/ https://physics.nist.gov/cuu/Constants/index.html

Expand Down Expand Up @@ -617,4 +617,4 @@ metricyarncount meter/gram
jewlerspoint 2 milligram



@nrnunits_stop@
24 changes: 24 additions & 0 deletions src/modlunit/units.cpp
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Expand Up @@ -2,6 +2,8 @@

#include <algorithm>
#include <string>
#include <string_view>
#include <fstream>

/* /local/src/master/nrn/src/modlunit/units.c,v 1.5 1997/11/24 16:19:13 hines Exp */
/* Mostly from Berkeley */
Expand Down Expand Up @@ -100,6 +102,23 @@ static int dumpflg;

static const char* pc;

static constexpr std::string_view embedded_nrnunits =
#include "embedded_nrnunits.lib"
;

// cross-platform workaround for:
// https://github.com/neuronsimulator/nrn/issues/3470
// the API requires a FILE handle instead of a std::string or similar
// so we write a temporary file
static FILE* open_embedded_nrnunits_as_file() {
auto tmp_path = std::string(std::tmpnam(nullptr));
auto out = std::ofstream(tmp_path, std::ios::out);
out.write(embedded_nrnunits.data(), embedded_nrnunits.size());
out.close();

return std::fopen(tmp_path.c_str(), "r");
}

static int Getc(FILE* inp) {
if (inp != stdin) {
return getc(inp);
Expand Down Expand Up @@ -565,6 +584,11 @@ void unit_init() {
}
#endif

// try to load the embedded one as a last resort
if (!inpfile) {
inpfile = open_embedded_nrnunits_as_file();
}

if (!inpfile) {
fprintf(stderr, "Set a MODLUNIT environment variable path to the units table file\n");
fprintf(stderr, "Cant open units table in either of:\n%s\n", buf);
Expand Down
2 changes: 2 additions & 0 deletions src/nrniv/CMakeLists.txt
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Expand Up @@ -48,6 +48,7 @@ add_dependencies(generated_source_files modlunit_generated_files)
add_executable(modlunit ${NRN_MODLUNIT_SRC_FILES} "${NRN_MODLUNIT_GEN}/lex.cpp"
"${NRN_MODLUNIT_GEN}/parse1.cpp")
add_dependencies(modlunit modlunit_generated_files)
target_include_directories(modlunit PRIVATE "${PROJECT_BINARY_DIR}/share/nrn/lib")

target_compile_definitions(modlunit PRIVATE NRNUNIT=1)
cpp_cc_configure_sanitizers(TARGET modlunit)
Expand Down Expand Up @@ -96,6 +97,7 @@ add_dependencies(generated_source_files nocmodl_generated_files)

add_executable(nocmodl ${NRN_NOCMODL_SRC_FILES} "${NRN_NOCMODL_GEN}/lex.cpp"
"${NRN_NOCMODL_GEN}/parse1.cpp" "${NRN_NOCMODL_GEN}/diffeq.cpp")
target_include_directories(nocmodl PRIVATE "${PROJECT_BINARY_DIR}/share/nrn/lib")
cpp_cc_configure_sanitizers(TARGET nocmodl)
add_dependencies(nocmodl nocmodl_generated_files)
target_compile_definitions(nocmodl PRIVATE COMPILE_DEFINITIONS NMODL=1 CVODE=1)
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8 changes: 7 additions & 1 deletion test/CMakeLists.txt
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Expand Up @@ -802,8 +802,14 @@ add_modlunit_test("${PROJECT_SOURCE_DIR}/src/nrnoc/hh.mod")
add_modlunit_test("${PROJECT_SOURCE_DIR}/src/nrnoc/stim.mod")
add_modlunit_test("${PROJECT_SOURCE_DIR}/src/nrnoc/pattern.mod")
add_modlunit_test("${PROJECT_SOURCE_DIR}/test/hoctests/rand.mod")
# Test nocmodl with units
add_test(
NAME nocmodl::no_env
COMMAND $<TARGET_FILE:nocmodl> -o "${CMAKE_CURRENT_BINARY_DIR}"
"${PROJECT_SOURCE_DIR}/test/coreneuron/mod files/axial.mod"
WORKING_DIRECTORY "${PROJECT_BINARY_DIR}")
set_property(TEST modlunit_pattern PROPERTY WILL_FAIL ON)

cpp_cc_configure_sanitizers(TEST nocmodl::no_env)
set_tests_properties(${TESTS} PROPERTIES ENVIRONMENT "${NRN_RUN_FROM_BUILD_DIR_ENV}")
cpp_cc_configure_sanitizers(TEST ${TESTS})
# If profiling is enabled, run ringtest with profiler
Expand Down
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