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implement running LAMMPS asynchonously in a separate thread

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This commit is contained in:
Axel Kohlmeyer
2023-07-27 02:56:07 -04:00
parent a62d1be3e6
commit da0669d988
8 changed files with 279 additions and 77 deletions
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2
tools/lammps-gui/CMakeLists.txt
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@ -69,6 +69,8 @@ set(PROJECT_SOURCES
lammpsgui.cpp
lammpsgui.h
lammpsgui.ui
lammpsrunner.cpp
lammpsrunner.h
stdcapture.cpp
${PLUGIN_LOADER_SRC}
)

3
tools/lammps-gui/TODO.md
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@ -7,7 +7,7 @@ LAMMPS-GUI TODO list:
- add "Help" entry to menu bar. Should open a popup window with a one page description of how to use it. Use HTML or Markdown text.
- add "View" entry to menu bar, where dialog windows may be enabled/disabled (e.g. Render)
- add dialog when exiting asking if file should be saved when it is modified
- add CTRL-q hotkey to log windows so you can exit the entire application
- add CTRL-q hotkey to log windows so you can exit the entire application (add do you really want to? dialog to this)
- add "render" dialog where a "write_dump image" can be triggered. dialog should offer options for size, zoom, rotation, colors(?)
- add "syntax check" with enabled "-skiprun" flag.
- add settings dialog where certain properties can be set through customizing the LAMMPS command line
@ -19,7 +19,6 @@ LAMMPS-GUI TODO list:
# Long term ideas
- support single stepping, i.e. process input line by line (need to detect continuation chars!) with highlighting active line(s)
- run LAMMMPS instance in a separate thread, modify capture to regularly poll pipe and retrieve/append output while job is running
- have command text input file in/above status bar where individual commands can be tested. have insert button to copy line into file at the current point
- support text completion as done with lammps-shell
- have context menu for known commands to offer retrieving help by dispatching URL to webbrowser (process index from sphinx for that purpose)

213
tools/lammps-gui/lammpsgui.cpp
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@ -12,18 +12,24 @@
------------------------------------------------------------------------- */
#include "lammpsgui.h"
#include "highlighter.h"
#include "lammpsrunner.h"
#include "stdcapture.h"
#include "ui_lammpsgui.h"
//#include <QApplication>
#include <QFileDialog>
#include <QFileInfo>
#include <QFont>
#include <QLabel>
#include <QMessageBox>
#include <QPlainTextEdit>
#include <QProgressBar>
#include <QShortcut>
#include <QStatusBar>
#include <QTextStream>
#include <QTimer>
#include <cstring>
#include <string>
#if defined(LAMMPS_GUI_USE_PLUGIN)
@ -33,7 +39,9 @@
#endif
LammpsGui::LammpsGui(QWidget *parent, const char *filename) :
QMainWindow(parent), ui(new Ui::LammpsGui), lammps_handle(nullptr), plugin_handle(nullptr)
QMainWindow(parent), ui(new Ui::LammpsGui), highlighter(nullptr), capturer(nullptr),
status(nullptr), logwindow(nullptr), logupdater(nullptr), progress(nullptr),
lammps_handle(nullptr), plugin_handle(nullptr), is_running(false)
{
ui->setupUi(this);
this->setCentralWidget(ui->textEdit);
@ -74,17 +82,21 @@ LammpsGui::LammpsGui(QWidget *parent, const char *filename) :
status = new QLabel("Ready.");
status->setFixedWidth(300);
ui->statusbar->addWidget(status);
progress = new QProgressBar();
progress->setRange(0, 1000);
progress->setFixedWidth(500);
ui->statusbar->addWidget(progress);
#if defined(LAMMPS_GUI_USE_PLUGIN)
liblammpsplugin_t *plugin = liblammpsplugin_load("liblammps.so");
if (!plugin) plugin = liblammpsplugin_load("liblammps.dylib");
if (!plugin) plugin = liblammpsplugin_load("liblammps.dll");
bool do_exit = !plugin || (plugin && plugin->abiversion != LAMMPSPLUGIN_ABI_VERSION);
if (!plugin) QMessageBox::critical(this, "Warning", "Cannot open LAMMPS shared library file");
if (plugin && (plugin->abiversion != LAMMPSPLUGIN_ABI_VERSION))
liblammpsplugin_t *lammps = liblammpsplugin_load("liblammps.so");
if (!lammps) lammps = liblammpsplugin_load("liblammps.dylib");
if (!lammps) lammps = liblammpsplugin_load("liblammps.dll");
bool do_exit = !lammps || (lammps && lammps->abiversion != LAMMPSPLUGIN_ABI_VERSION);
if (!lammps) QMessageBox::critical(this, "Warning", "Cannot open LAMMPS shared library file");
if (lammps && (lammps->abiversion != LAMMPSPLUGIN_ABI_VERSION))
QMessageBox::critical(this, "Warning",
"ERROR: LAMMPS lib plugin ABI version does not match");
plugin_handle = plugin;
plugin_handle = lammps;
if (do_exit) exit(1);
#endif
}
@ -95,6 +107,7 @@ LammpsGui::~LammpsGui()
delete highlighter;
delete capturer;
delete status;
delete logwindow;
}
void LammpsGui::new_document()
@ -176,11 +189,11 @@ void LammpsGui::quit()
{
#if defined(LAMMPS_GUI_USE_PLUGIN)
if (lammps_handle) {
liblammpsplugin_t *plugin = (liblammpsplugin_t *)plugin_handle;
plugin->close(lammps_handle);
plugin->mpi_finalize();
plugin->kokkos_finalize();
plugin->python_finalize();
liblammpsplugin_t *lammps = (liblammpsplugin_t *)plugin_handle;
lammps->close(lammps_handle);
lammps->mpi_finalize();
lammps->kokkos_finalize();
lammps->python_finalize();
}
#else
if (lammps_handle) {
@ -224,6 +237,79 @@ void LammpsGui::redo()
ui->textEdit->redo();
}
void LammpsGui::logupdate()
{
double t_elapsed, t_remain, t_total;
int completed = 1000;
if (is_running) {
#if defined(LAMMPS_GUI_USE_PLUGIN)
liblammpsplugin_t *lammps = (liblammpsplugin_t *)plugin_handle;
if (lammps->is_running(lammps_handle)) {
t_elapsed = lammps->get_thermo(lammps_handle, "cpu");
t_remain = lammps->get_thermo(lammps_handle, "cpuremain");
t_total = t_elapsed + t_remain + 1.0e-10;
completed = t_elapsed / t_total * 1000.0;
}
#else
if (lammps_is_running(lammps_handle)) {
t_elapsed = lammps_get_thermo(lammps_handle, "cpu");
t_remain = lammps_get_thermo(lammps_handle, "cpuremain");
t_total = t_elapsed + t_remain + 1.0e-10;
completed = t_elapsed / t_total * 1000.0;
}
#endif
}
progress->setValue(completed);
if (logwindow) {
const auto text = capturer->GetChunk();
if (text.size() > 0) {
logwindow->insertPlainText(text.c_str());
logwindow->moveCursor(QTextCursor::End);
logwindow->textCursor().deleteChar();
}
}
}
void LammpsGui::run_done()
{
logupdater->stop();
delete logupdater;
logupdater = nullptr;
progress->setValue(1000);
capturer->EndCapture();
auto log = capturer->GetCapture();
logwindow->insertPlainText(log.c_str());
logwindow->moveCursor(QTextCursor::End);
bool success = true;
constexpr int BUFLEN = 1024;
char errorbuf[BUFLEN];
#if defined(LAMMPS_GUI_USE_PLUGIN)
liblammpsplugin_t *lammps = (liblammpsplugin_t *)plugin_handle;
if (lammps->has_error(lammps_handle)) {
lammps->get_last_error_message(lammps_handle, errorbuf, BUFLEN);
success = false;
}
#else
if (lammps_has_error(lammps_handle)) {
lammps_get_last_error_message(lammps_handle, errorbuf, BUFLEN);
success = false;
}
#endif
if (success) {
status->setText("Ready.");
} else {
status->setText("Failed.");
QMessageBox::critical(this, "LAMMPS-GUI Error",
QString("Error running LAMMPS:\n\n") + errorbuf);
}
is_running = false;
}
void LammpsGui::run_buffer()
{
status->setText("Running LAMMPS. Please wait...");
@ -232,51 +318,38 @@ void LammpsGui::run_buffer()
if (!lammps_handle) return;
clear();
capturer->BeginCapture();
std::string buffer = ui->textEdit->toPlainText().toStdString();
#if defined(LAMMPS_GUI_USE_PLUGIN)
liblammpsplugin_t *plugin = (liblammpsplugin_t *)plugin_handle;
plugin->commands_string(lammps_handle, buffer.c_str());
#else
lammps_commands_string(lammps_handle, buffer.c_str());
#endif
capturer->EndCapture();
auto log = capturer->GetCapture();
status->setText("Ready.");
auto box = new QPlainTextEdit();
box->document()->setPlainText(log.c_str());
box->setReadOnly(true);
box->setWindowTitle("LAMMPS-GUI - Output from running LAMMPS on buffer - " + current_file);
std::string buffer = ui->textEdit->toPlainText().toStdString();
char *input = new char[buffer.size() + 1];
memcpy(input, buffer.c_str(), buffer.size() + 1);
is_running = true;
LammpsRunner *runner = new LammpsRunner(this);
runner->setup_run(lammps_handle, input, plugin_handle);
connect(runner, &LammpsRunner::resultReady, this, &LammpsGui::run_done);
connect(runner, &LammpsRunner::finished, runner, &QObject::deleteLater);
runner->start();
logwindow = new QPlainTextEdit();
logwindow->setReadOnly(true);
logwindow->setCenterOnScroll(true);
logwindow->moveCursor(QTextCursor::End);
logwindow->setWindowTitle("LAMMPS-GUI - Output from running LAMMPS on buffer - " +
current_file);
QFont text_font;
text_font.setFamilies(QStringList({"Consolas", "Monospace", "Sans", "Courier"}));
text_font.setFixedPitch(true);
text_font.setStyleHint(QFont::TypeWriter);
box->document()->setDefaultFont(text_font);
box->setLineWrapMode(QPlainTextEdit::NoWrap);
box->setMinimumSize(800, 600);
QShortcut *shortcut = new QShortcut(QKeySequence(Qt::CTRL + Qt::Key_W), box);
QObject::connect(shortcut, &QShortcut::activated, box, &QPlainTextEdit::close);
box->show();
logwindow->document()->setDefaultFont(text_font);
logwindow->setLineWrapMode(QPlainTextEdit::NoWrap);
logwindow->setMinimumSize(800, 600);
QShortcut *shortcut = new QShortcut(QKeySequence(Qt::CTRL + Qt::Key_W), logwindow);
QObject::connect(shortcut, &QShortcut::activated, logwindow, &QPlainTextEdit::close);
logwindow->show();
#if defined(LAMMPS_GUI_USE_PLUGIN)
if (plugin->has_error(lammps_handle)) {
constexpr int BUFLEN = 1024;
char errorbuf[BUFLEN];
plugin->get_last_error_message(lammps_handle, errorbuf, BUFLEN);
QMessageBox::critical(this, "LAMMPS-GUI Error",
QString("Error running LAMMPS:\n\n") + errorbuf);
}
#else
if (lammps_has_error(lammps_handle)) {
constexpr int BUFLEN = 1024;
char errorbuf[BUFLEN];
lammps_get_last_error_message(lammps_handle, errorbuf, BUFLEN);
QMessageBox::critical(this, "LAMMPS-GUI Error",
QString("Error running LAMMPS:\n\n") + errorbuf);
}
#endif
logupdater = new QTimer(this);
connect(logupdater, &QTimer::timeout, this, &LammpsGui::logupdate);
logupdater->start(1000);
}
void LammpsGui::clear()
@ -293,23 +366,29 @@ void LammpsGui::clear()
void LammpsGui::about()
{
start_lammps();
std::string version = "This is LAMMPS-GUI version 0.1";
capturer->BeginCapture();
std::string info = "LAMMPS is currently running. LAMMPS config info not available.";
// LAMMPS is not re-entrant, so we can only query LAMMPS when it is not running
if (!is_running) {
start_lammps();
capturer->BeginCapture();
#if defined(LAMMPS_GUI_USE_PLUGIN)
((liblammpsplugin_t *)plugin_handle)->commands_string(lammps_handle, "info config");
((liblammpsplugin_t *)plugin_handle)->commands_string(lammps_handle, "info config");
#else
lammps_commands_string(lammps_handle, "info config");
lammps_commands_string(lammps_handle, "info config");
#endif
capturer->EndCapture();
std::string info = capturer->GetCapture();
auto start = info.find("LAMMPS version:");
auto end = info.find("Info-Info-Info", start);
capturer->EndCapture();
info = capturer->GetCapture();
auto start = info.find("LAMMPS version:");
auto end = info.find("Info-Info-Info", start);
info = std::string(info, start, end - start);
}
QMessageBox msg;
msg.setWindowTitle("About LAMMPS-GUI");
msg.setText(version.c_str());
msg.setInformativeText(std::string(info, start, end - start).c_str());
msg.setInformativeText(info.c_str());
msg.setIcon(QMessageBox::NoIcon);
msg.setStandardButtons(QMessageBox::Ok);
QFont font;
@ -328,14 +407,14 @@ void LammpsGui::start_lammps()
int nargs = sizeof(args) / sizeof(char *);
#if defined(LAMMPS_GUI_USE_PLUGIN)
liblammpsplugin_t *plugin = (liblammpsplugin_t *)plugin_handle;
liblammpsplugin_t *lammps = (liblammpsplugin_t *)plugin_handle;
// Create LAMMPS instance if not already present
if (!lammps_handle) lammps_handle = plugin->open_no_mpi(nargs, args, nullptr);
if (plugin->has_error(lammps_handle)) {
if (!lammps_handle) lammps_handle = lammps->open_no_mpi(nargs, args, nullptr);
if (lammps->has_error(lammps_handle)) {
constexpr int BUFLEN = 1024;
char errorbuf[BUFLEN];
plugin->get_last_error_message(lammps_handle, errorbuf, BUFLEN);
lammps->get_last_error_message(lammps_handle, errorbuf, BUFLEN);
QMessageBox::critical(this, "LAMMPS-GUI Error",
QString("Error launching LAMMPS:\n\n") + errorbuf);

12
tools/lammps-gui/lammpsgui.h
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@ -16,7 +16,6 @@
#include <QMainWindow>
#include <QString>
#include <QLabel>
// forward declarations
@ -26,6 +25,11 @@ class LammpsGui;
}
QT_END_NAMESPACE
class QLabel;
class QPlainTextEdit;
class QProgressBar;
class QTimer;
class Highlighter;
class StdCapture;
@ -40,6 +44,7 @@ protected:
void open_file(const QString &filename);
void write_file(const QString &filename);
void start_lammps();
void run_done();
private slots:
void new_document();
@ -55,17 +60,22 @@ private slots:
void clear();
void run_buffer();
void about();
void logupdate();
private:
Ui::LammpsGui *ui;
Highlighter *highlighter;
StdCapture *capturer;
QLabel *status;
QPlainTextEdit *logwindow;
QTimer *logupdater;
QProgressBar *progress;
QString current_file;
QString current_dir;
void *lammps_handle;
void *plugin_handle;
bool is_running;
};
#endif // LAMMPSGUI_H

44
tools/lammps-gui/lammpsrunner.cpp Normal file
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@ -0,0 +1,44 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "lammpsrunner.h"
#if defined(LAMMPS_GUI_USE_PLUGIN)
#include "liblammpsplugin.h"
#else
#include "library.h"
#endif
#include <cstdio>
LammpsRunner::LammpsRunner(QObject *parent) :
QThread(parent), handle(nullptr), plugin(nullptr), input(nullptr)
{
}
void LammpsRunner::run()
{
if (handle) {
#if defined(LAMMPS_GUI_USE_PLUGIN)
liblammpsplugin_t *lammps = (liblammpsplugin_t *)plugin;
lammps->commands_string(handle, input);
#else
lammps_commands_string(handle, input);
#endif
}
emit resultReady();
}
// Local Variables:
// c-basic-offset: 4
// End:

48
tools/lammps-gui/lammpsrunner.h Normal file
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@ -0,0 +1,48 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LAMMPSRUNNER_H
#define LAMMPSRUNNER_H
#include <QThread>
class LammpsRunner : public QThread {
Q_OBJECT
public:
LammpsRunner(QObject *parent = nullptr);
~LammpsRunner() = default;
// execute LAMMPS run in runner thread
void run() override;
// transfer info to worker thread
void setup_run(void *_handle, const char *_input, void *_plugin = nullptr)
{
handle = _handle;
plugin = _plugin;
input = _input;
}
signals:
void resultReady();
private:
void *handle, *plugin;
const char *input;
};
#endif
// Local Variables:
// c-basic-offset: 4
// End:

28
tools/lammps-gui/stdcapture.cpp
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@ -24,7 +24,6 @@
#define dup2 _dup2
#define fileno _fileno
#define close _close
#define pipe _pipe
#define read _read
#define eof _eof
#else
@ -44,9 +43,9 @@ StdCapture::StdCapture() : m_oldStdOut(0), m_capturing(false)
m_pipe[READ] = 0;
m_pipe[WRITE] = 0;
#if _WIN32
if (pipe(m_pipe, 65536, O_BINARY) == -1) return;
if (_pipe(m_pipe, 65536, O_BINARY) == -1) return;
#else
if (pipe(m_pipe) == -1) return;
if (pipe2(m_pipe, O_NONBLOCK) == -1) return;
#endif
m_oldStdOut = dup(fileno(stdout));
if (m_oldStdOut == -1) return;
@ -75,8 +74,6 @@ bool StdCapture::EndCapture()
dup2(m_oldStdOut, fileno(stdout));
m_captured.clear();
constexpr int bufSize = 1025;
char buf[bufSize];
int bytesRead;
bool fd_blocked;
@ -104,7 +101,26 @@ bool StdCapture::EndCapture()
return true;
}
std::string StdCapture::GetCapture() const
std::string StdCapture::GetChunk()
{
if (!m_capturing) return std::string();
int bytesRead = 0;
buf[0] = '\0';
#ifdef _WIN32
if (!eof(m_pipe[READ])) {
bytesRead = read(m_pipe[READ], buf, bufSize - 1);
}
#else
bytesRead = read(m_pipe[READ], buf, bufSize - 1);
#endif
if (bytesRead > 0) {
buf[bytesRead] = '\0';
}
return std::string(buf);
}
std::string StdCapture::GetCapture()
{
std::string::size_type idx = m_captured.find_last_not_of("\r\n");
if (idx == std::string::npos) {

6
tools/lammps-gui/stdcapture.h
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@ -23,7 +23,8 @@ public:
void BeginCapture();
bool EndCapture();
std::string GetCapture() const;
std::string GetCapture();
std::string GetChunk();
private:
enum PIPES { READ, WRITE };
@ -32,6 +33,9 @@ private:
bool m_capturing;
bool m_init;
std::string m_captured;
static constexpr int bufSize = 1025;
char buf[bufSize];
};
#endif