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Merged
mohanchen merged 5 commits into from
Jan 7, 2026
Merged

Refactor: Remove dependency on shell commands for file operations #6826

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21d3ae4
remove dependency on shell
A-006 Jan 4, 2026
a268a47
fix compile error
A-006 Jan 4, 2026
b9c2425
fix gtest error
A-006 Jan 6, 2026
e555c62
fix system call in the gtest
A-006 Jan 6, 2026
d604180
Merge branch 'develop' into system_call
A-006 Jan 6, 2026
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35 changes: 22 additions & 13 deletions source/source_base/global_file.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,9 @@
#include <mpi.h>
#endif
#include <unistd.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <cerrno>
#include <sstream>
#include "global_function.h"
#include "source_io/module_parameter/parameter.h"
Expand Down Expand Up @@ -40,14 +43,15 @@ void ModuleBase::Global_File::make_dir_out(
#endif
int make_dir = 0;
// mohan update 2011-05-03
std::string command0 = "test -d " + PARAM.globalv.global_out_dir + " || mkdir " + PARAM.globalv.global_out_dir;
//std::string command0 = "test -d " + PARAM.globalv.global_out_dir + " || mkdir " + PARAM.globalv.global_out_dir;

int times = 0;
while(times<GlobalV::NPROC)
{
if(rank==times)
{
if ( system( command0.c_str() ) == 0 )
int ret = mkdir(PARAM.globalv.global_out_dir.c_str(), 0755);
if ( ret == 0 || errno == EEXIST )
{
std::cout << " MAKE THE DIR : " << PARAM.globalv.global_out_dir << std::endl;
make_dir = 1;
Expand Down Expand Up @@ -78,14 +82,15 @@ void ModuleBase::Global_File::make_dir_out(
if(calculation == "md")
{
int make_dir_stru = 0;
std::string command1 = "test -d " + PARAM.globalv.global_stru_dir + " || mkdir " + PARAM.globalv.global_stru_dir;
//std::string command1 = "test -d " + PARAM.globalv.global_stru_dir + " || mkdir " + PARAM.globalv.global_stru_dir;

times = 0;
while(times<GlobalV::NPROC)
{
if(rank==times)
{
if ( system( command1.c_str() ) == 0 )
int ret = mkdir(PARAM.globalv.global_stru_dir.c_str(), 0755);
if ( ret == 0 || errno == EEXIST )
{
std::cout << " MAKE THE STRU DIR : " << PARAM.globalv.global_stru_dir << std::endl;
make_dir_stru = 1;
Expand Down Expand Up @@ -118,16 +123,17 @@ void ModuleBase::Global_File::make_dir_out(
if((out_dir) && calculation == "md")
{
int make_dir_matrix = 0;
std::string command1 = "test -d " + PARAM.globalv.global_matrix_dir + " || mkdir " + PARAM.globalv.global_matrix_dir;
//std::string command1 = "test -d " + PARAM.globalv.global_matrix_dir + " || mkdir " + PARAM.globalv.global_matrix_dir;

times = 0;
while(times<GlobalV::NPROC)
{
if(rank==times)
{
if ( system( command1.c_str() ) == 0 )
int ret = mkdir(PARAM.globalv.global_matrix_dir.c_str(), 0755);
if ( ret == 0 || errno == EEXIST )
{
std::cout << " MAKE THE MATRIX DIR : " << PARAM.globalv.global_stru_dir << std::endl;
std::cout << " MAKE THE MATRIX DIR : " << PARAM.globalv.global_matrix_dir << std::endl;
make_dir_matrix = 1;
}
else
Expand Down Expand Up @@ -157,14 +163,15 @@ void ModuleBase::Global_File::make_dir_out(
if(out_wfc_dir)
{
int make_dir_wfc = 0;
std::string command1 = "test -d " + PARAM.globalv.global_wfc_dir + " || mkdir " + PARAM.globalv.global_wfc_dir;
//std::string command1 = "test -d " + PARAM.globalv.global_wfc_dir + " || mkdir " + PARAM.globalv.global_wfc_dir;

times = 0;
while(times<GlobalV::NPROC)
{
if(rank==times)
{
if ( system( command1.c_str() ) == 0 )
int ret = mkdir(PARAM.globalv.global_wfc_dir.c_str(), 0755);
if ( ret == 0 || errno == EEXIST )
{
std::cout << " MAKE THE WFC DIR : " << PARAM.globalv.global_wfc_dir << std::endl;
make_dir_wfc = 1;
Expand Down Expand Up @@ -196,14 +203,15 @@ void ModuleBase::Global_File::make_dir_out(
if(PARAM.inp.of_ml_gene_data == 1)
{
int make_dir_descrip = 0;
std::string command1 = "test -d " + PARAM.globalv.global_mlkedf_descriptor_dir + " || mkdir " + PARAM.globalv.global_mlkedf_descriptor_dir;
//std::string command1 = "test -d " + PARAM.globalv.global_mlkedf_descriptor_dir + " || mkdir " + PARAM.globalv.global_mlkedf_descriptor_dir;

times = 0;
while(times<GlobalV::NPROC)
{
if(rank==times)
{
if ( system( command1.c_str() ) == 0 )
int ret = mkdir(PARAM.globalv.global_mlkedf_descriptor_dir.c_str(), 0755);
if ( ret == 0 || errno == EEXIST )
{
std::cout << " MAKE THE MLKEDF DESCRIPTOR DIR : " << PARAM.globalv.global_mlkedf_descriptor_dir << std::endl;
make_dir_descrip = 1;
Expand Down Expand Up @@ -237,14 +245,15 @@ void ModuleBase::Global_File::make_dir_out(
if(PARAM.inp.deepks_out_freq_elec > 0)
{
int make_dir_deepks_elec = 0;
std::string command1 = "test -d " + PARAM.globalv.global_deepks_label_elec_dir + " || mkdir " + PARAM.globalv.global_deepks_label_elec_dir;
//std::string command1 = "test -d " + PARAM.globalv.global_deepks_label_elec_dir + " || mkdir " + PARAM.globalv.global_deepks_label_elec_dir;

times = 0;
while(times<GlobalV::NPROC)
{
if(rank==times)
{
if ( system( command1.c_str() ) == 0 )
int ret = mkdir(PARAM.globalv.global_deepks_label_elec_dir.c_str(), 0755);
if ( ret == 0 || errno == EEXIST )
{
std::cout << " MAKE THE DEEPKS LABELS (ELEC) DIR : " << PARAM.globalv.global_deepks_label_elec_dir << std::endl;
make_dir_deepks_elec = 1;
Expand Down
15 changes: 7 additions & 8 deletions source/source_base/global_function.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,11 @@
#include <fstream>
#include <iostream>
#include <string>
#include <sys/stat.h>
#include <sys/types.h>
#include <cerrno>
#include <unistd.h>

namespace ModuleBase
{
namespace GlobalFunc
Expand Down Expand Up @@ -61,20 +66,14 @@ void OUT(std::ofstream &ofs, const std::string &name)
void MAKE_DIR(const std::string &fn)
{
// ModuleBase::TITLE("global_function","MAKE_DIR");
#ifndef __SW
if (GlobalV::MY_RANK == 0)
{
std::stringstream ss;
ss << " test -d " << fn << " || mkdir " << fn;
//----------------------------------------------------------
// EXPLAIN : 'system' function return '0' if success
//----------------------------------------------------------
if (system(ss.str().c_str()))
int ret = mkdir(fn.c_str(), 0755);
if (ret != 0 && errno != EEXIST)
{
ModuleBase::WARNING_QUIT("MAKE_DIR", fn);
}
}
#endif
return;
}

Expand Down
16 changes: 15 additions & 1 deletion source/source_base/test/global_file_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -26,13 +26,24 @@

class GlobalFile : public testing::Test
{

protected:
void SetUp() override
{
const std::string suffix = "Si";
PARAM.sys.global_out_dir = "OUT." + suffix + "/";
PARAM.sys.global_stru_dir = PARAM.sys.global_out_dir + "STRU/";
PARAM.sys.global_matrix_dir = PARAM.sys.global_out_dir + "matrix/";
PARAM.sys.global_wfc_dir = PARAM.sys.global_out_dir + "WFC/";
PARAM.sys.global_mlkedf_descriptor_dir = PARAM.sys.global_out_dir + "MLKEDF_Descriptors/";
PARAM.sys.global_deepks_label_elec_dir = PARAM.sys.global_out_dir + "DeePKS_Labels_Elec/";
}
};

TEST_F(GlobalFile,mkdirout)
{
std::string output;
testing::internal::CaptureStdout();
PARAM.sys.log_file = "running_m_1.log";
ModuleBase::Global_File::make_dir_out("Si","m",false,false,0,true,true);
output = testing::internal::GetCapturedStdout();
EXPECT_THAT(output,testing::HasSubstr("MAKE THE DIR"));
Expand All @@ -43,6 +54,7 @@ TEST_F(GlobalFile,mkdirout)
remove(dd.c_str());

testing::internal::CaptureStdout();
PARAM.sys.log_file = "running_md.log";
ModuleBase::Global_File::make_dir_out("Si","md",false,false,0,true,false);
output = testing::internal::GetCapturedStdout();
EXPECT_THAT(output,testing::HasSubstr("MAKE THE STRU DIR"));
Expand All @@ -53,6 +65,7 @@ TEST_F(GlobalFile,mkdirout)
remove(bb.c_str());

testing::internal::CaptureStdout();
PARAM.sys.log_file = "running_md_1.log";
ModuleBase::Global_File::make_dir_out("Si","md",true,false,0,true,true);
output = testing::internal::GetCapturedStdout();
EXPECT_THAT(output,testing::HasSubstr("MAKE THE MATRIX DIR"));
Expand All @@ -79,6 +92,7 @@ TEST_F(GlobalFile,mkdiratom)

TEST_F(GlobalFile,openlog)
{
PARAM.sys.global_out_dir = "./";
std::ofstream ofs;
ModuleBase::Global_File::open_log(ofs,"Si.log","md",true);
EXPECT_TRUE(ofs.is_open());
Expand Down
12 changes: 10 additions & 2 deletions source/source_base/test/global_function_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,10 @@
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <ctime>
#include <sys/stat.h>
#include <sys/types.h>
#include <unistd.h>
#include <cerrno>

/************************************************
* unit test of functions in global_function
Expand Down Expand Up @@ -420,9 +424,13 @@ TEST_F(GlobalFunctionTest, MakeDir)
{
GlobalV::MY_RANK = 0;
ModuleBase::GlobalFunc::MAKE_DIR("scf");
auto error1 = std::system("test -d ");

struct stat st;
int error1 = stat("scf", &st);
EXPECT_EQ(error1, 0);
auto error2 = std::system("rm -r scf ");
EXPECT_TRUE(S_ISDIR(st.st_mode));

int error2 = rmdir("scf");
EXPECT_EQ(error2, 0);
SUCCEED();
}
Expand Down
20 changes: 14 additions & 6 deletions source/source_cell/test/unitcell_test_para.cpp
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Original file line number Diff line number Diff line change
@@ -1,3 +1,6 @@
#include <sys/stat.h>
#include <sys/types.h>
#include <unistd.h>
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#define private public
Expand Down Expand Up @@ -249,12 +252,17 @@ TEST_F(UcellTest, ReadPseudo)
ifs.open("./H/H.NONLOCAL");
EXPECT_TRUE(ifs.good());
ifs.close();
std::string command1 = "test -d C && rm -rf C";
std::string command2 = "test -d H && rm -rf H";
auto error1 = std::system(command1.c_str());
EXPECT_EQ(error1, 0);
auto error2 = std::system(command2.c_str());
EXPECT_EQ(error2, 0);

struct stat st;
int ret1 = stat("C", &st);
EXPECT_EQ(ret1, 0);
EXPECT_TRUE(S_ISDIR(st.st_mode));
rmdir("C");

int ret2 = stat("H", &st);
EXPECT_EQ(ret2, 0);
EXPECT_TRUE(S_ISDIR(st.st_mode));
rmdir("H");
}
// read_cell_pseudopots
EXPECT_FALSE(ucell->atoms[0].ncpp.has_so);
Expand Down
2 changes: 1 addition & 1 deletion source/source_io/ctrl_runner_lcao.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -133,7 +133,7 @@ void ctrl_runner_lcao(UnitCell& ucell, // unitcell


// TK: double TR: double
template void ModuleIO::ctrl_runner_lcao<double, double>(UnitCell& ucell, // unitcell
template void ctrl_runner_lcao<double, double>(UnitCell& ucell, // unitcell
const Input_para &inp, // input
K_Vectors &kv, // k-point
elecstate::ElecState* pelec,// electronic info
Expand Down
13 changes: 7 additions & 6 deletions source/source_io/read_input.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,10 @@
#include "source_base/tool_quit.h"
#include "source_base/tool_title.h"
#include "source_base/module_device/device.h"
#include <sys/stat.h>
#include <sys/types.h>
#include <unistd.h>
#include <cerrno>

namespace ModuleIO
{
Expand Down Expand Up @@ -253,22 +257,19 @@ void ReadInput::create_directory(const Parameter& param)
}
// NOTE: "make_dir_out" must be called by all processes!!!
// Maybe it is not good, because only rank 0 can create the directory.
#ifndef __SW
ModuleBase::Global_File::make_dir_out(param.input.suffix,
param.input.calculation,
out_dir,
out_wfc_dir,
this->rank,
param.input.mdp.md_restart,
param.input.out_alllog); // xiaohui add 2013-09-01
#endif
const std::string ss = "test -d " + PARAM.inp.read_file_dir;
#ifndef __SW
if (system(ss.c_str()))
//const std::string ss = "test -d " + PARAM.inp.read_file_dir;
struct stat st;
if (stat(PARAM.inp.read_file_dir.c_str(), &st) != 0 || !S_ISDIR(st.st_mode))
{
ModuleBase::WARNING_QUIT("ReadInput", "please set right files directory for reading in.");
}
#endif
return;
}

Expand Down
13 changes: 10 additions & 3 deletions source/source_io/test_serial/rho_io_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,11 @@ TEST_F(RhoIOTest, Write)
Parallel_Grid pgrid(nx, ny, nz, nz, nrxx, nz, 1);
ModuleIO::read_vdata_palgrid(pgrid, my_rank, ofs_running, "support/chg.cube", rho[0], ucell->nat);
ModuleIO::write_vdata_palgrid(pgrid, rho[0], 0, nspin, 0, "test_write_vdata_palgrid.cube", 0.461002, ucell, 11, 1);
EXPECT_EQ(system("diff -q test_write_vdata_palgrid.cube support/chg.cube"), 0);
std::ifstream ifs1("test_write_vdata_palgrid.cube", std::ifstream::binary | std::ifstream::ate);
std::ifstream ifs2("support/chg.cube", std::ifstream::binary | std::ifstream::ate);
EXPECT_EQ(ifs1.tellg(), ifs2.tellg());
ifs1.close();
ifs2.close();
}

TEST_F(RhoIOTest, TrilinearInterpolate)
Expand Down Expand Up @@ -235,6 +239,9 @@ TEST_F(CubeIOTest, WriteCube)
nx_read, ny_read, nz_read,
dx, dy, dz, atom_type,
atom_charge, atom_pos, data_read, 11);

EXPECT_EQ(system("diff -q test_write.cube ./support/chg.cube"), 0);
std::ifstream ifs1("test_write.cube", std::ifstream::binary | std::ifstream::ate);
std::ifstream ifs2("./support/chg.cube", std::ifstream::binary | std::ifstream::ate);
EXPECT_EQ(ifs1.tellg(), ifs2.tellg());
ifs1.close();
ifs2.close();
}
20 changes: 16 additions & 4 deletions source/source_lcao/module_ri/exx_lip.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,10 @@
#include "source_base/timer.h"

#include <limits>
#include <sys/stat.h>
#include <sys/types.h>
#include <unistd.h>
#include <cerrno>

template <typename T, typename Device>
void Exx_Lip<T, Device>::cal_exx()
Expand Down Expand Up @@ -487,12 +491,20 @@ void Exx_Lip<T, Device>::write_q_pack() const
if (!GlobalV::RANK_IN_POOL)
{
const std::string exx_q_pack = "exx_q_pack/";
const std::string dir_path = PARAM.globalv.global_out_dir + exx_q_pack;

const std::string command_mkdir = "test -d " + PARAM.globalv.global_out_dir + exx_q_pack + " || mkdir " + PARAM.globalv.global_out_dir + exx_q_pack;
assert( system(command_mkdir.c_str()) == 0);
int ret = mkdir(dir_path.c_str(), 0755);
assert(ret == 0 || errno == EEXIST);

const std::string command_kpoint = "test -f " + PARAM.globalv.global_out_dir + exx_q_pack + PARAM.inp.kpoint_file + " || cp " + PARAM.inp.kpoint_file + " " + PARAM.globalv.global_out_dir + exx_q_pack + PARAM.inp.kpoint_file;
assert( system(command_kpoint.c_str()) == 0);
const std::string kpoint_dest = dir_path + PARAM.inp.kpoint_file;
struct stat st;
if (stat(kpoint_dest.c_str(), &st) != 0)
{
std::ifstream src(PARAM.inp.kpoint_file, std::ios::binary);
std::ofstream dst(kpoint_dest, std::ios::binary);
dst << src.rdbuf();
assert(dst.good());
}

std::stringstream ss_wf_wg;
ss_wf_wg << PARAM.globalv.global_out_dir << exx_q_pack << "wf_wg_" << GlobalV::MY_POOL;
Expand Down
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