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Merge pull request #2727 from akohlmey/refactor-read-lines-from-file

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Move "read_lines_from_file" utility function from Comm class to utils namespace
This commit is contained in:
Axel Kohlmeyer
2021-04-26 13:24:24 -04:00
committed by GitHub
parent 4a2816b61c b0cd6b3ef7
commit 31d244dd80
14 changed files with 142 additions and 108 deletions
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20
doc/src/Developer_utils.rst
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@ -12,11 +12,18 @@ reduces redundant implementations and encourages consistent behavior.
I/O with status check
^^^^^^^^^^^^^^^^^^^^^
These are wrappers around the corresponding C library calls like
``fgets()`` or ``fread()``. They will check if there were errors
on reading or an unexpected end-of-file state was reached. In that
case, the functions will stop the calculation with an error message,
indicating the name of the problematic file, if possible.
The the first two functions are wrappers around the corresponding C
library calls ``fgets()`` or ``fread()``. They will check if there
were errors on reading or an unexpected end-of-file state was reached.
In that case, the functions will stop with an error message, indicating
the name of the problematic file, if possible unless the *error* argument
is a NULL pointer.
The :cpp:func:`read_lines_from_file` function will read the requested
number of lines of a maximum length into a buffer and will return 0
if successful or 1 if not. It also guarantees that all lines are
terminated with a newline character and the entire buffer with a
NULL character.
----------
@ -26,6 +33,9 @@ indicating the name of the problematic file, if possible.
.. doxygenfunction:: sfread
:project: progguide
.. doxygenfunction:: read_lines_from_file
:project: progguide
----------
String to number conversions with validity check

2
doc/utils/sphinx-config/false_positives.txt
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@ -2190,6 +2190,7 @@ nl
nlayers
nlen
Nlines
nlines
nlo
nlocal
Nlocal
@ -2281,6 +2282,7 @@ Ntype
ntypes
Ntypes
nucleotides
nullptr
num
numa
numactl

4
lib/atc/LammpsInterface.cpp
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@ -26,6 +26,7 @@
#include "bond.h" // bond potentials
#include "comm.h" //
#include "fix.h"
#include "utils.h"
// ATC includes
#include "ATC_Error.h"
@ -47,6 +48,7 @@ using std::pair;
using std::string;
using std::set;
using LAMMPS_NS::bigint;
using LAMMPS_NS::utils::read_lines_from_file;
namespace ATC {
@ -236,7 +238,7 @@ std::string LammpsInterface::read_file(std::string filename) const
std::stringstream s;
bool eof = false;
while ( ! eof) {
eof = lammps_->comm->read_lines_from_file(fp,1,MAXLINE,buffer);
eof = read_lines_from_file(fp,1,MAXLINE,buffer,comm_rank(),lammps_->world);
s << buffer;
}
fclose(fp);

5
src/REPLICA/neb.cpp
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@ -436,9 +436,10 @@ void NEB::readfile(char *file, int flag)
while (nread < nlines) {
nchunk = MIN(nlines-nread,CHUNK);
if (flag == 0)
eofflag = comm->read_lines_from_file_universe(fp,nchunk,MAXLINE,buffer);
eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,
universe->me,universe->uworld);
else
eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eofflag) error->all(FLERR,"Unexpected end of NEB file");
buf = buffer;

2
src/RIGID/fix_rigid.cpp
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@ -2302,7 +2302,7 @@ void FixRigid::readfile(int which, double *vec,
int nread = 0;
while (nread < nlines) {
nchunk = MIN(nlines-nread,CHUNK);
eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eofflag) error->all(FLERR,"Unexpected end of fix rigid file");
buf = buffer;

2
src/RIGID/fix_rigid_small.cpp
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@ -2475,7 +2475,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
int nread = 0;
while (nread < nlines) {
nchunk = MIN(nlines-nread,CHUNK);
eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eofflag) error->all(FLERR,"Unexpected end of fix rigid/small file");
buf = buffer;

5
src/SPIN/neb_spin.cpp
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@ -430,9 +430,10 @@ void NEBSpin::readfile(char *file, int flag)
while (nread < nlines) {
nchunk = MIN(nlines-nread,CHUNK);
if (flag == 0)
eofflag = comm->read_lines_from_file_universe(fp,nchunk,MAXLINE,buffer);
eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,
universe->me,universe->uworld);
else
eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
eofflag = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eofflag) error->all(FLERR,"Unexpected end of neb/spin file");
buf = buffer;

68
src/comm.cpp
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@ -1240,71 +1240,3 @@ void Comm::rendezvous_stats(int n, int nout, int nrvous, int nrvous_out,
utils::logmesg(lmp,mesg);
}
}
/* ----------------------------------------------------------------------
proc 0 reads Nlines from file into buf and bcasts buf to all procs
caller allocates buf to max size needed
each line is terminated by newline, even if last line in file is not
return 0 if successful, 1 if get EOF error before read is complete
------------------------------------------------------------------------- */
int Comm::read_lines_from_file(FILE *fp, int nlines, int maxline, char *buf)
{
int m;
if (me == 0) {
m = 0;
for (int i = 0; i < nlines; i++) {
if (!fgets(&buf[m],maxline,fp)) {
m = 0;
break;
}
m += strlen(&buf[m]);
}
if (m) {
if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
m++;
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
if (m == 0) return 1;
MPI_Bcast(buf,m,MPI_CHAR,0,world);
return 0;
}
/* ----------------------------------------------------------------------
proc 0 reads Nlines from file into buf and bcasts buf to all procs
caller allocates buf to max size needed
each line is terminated by newline, even if last line in file is not
return 0 if successful, 1 if get EOF error before read is complete
------------------------------------------------------------------------- */
int Comm::read_lines_from_file_universe(FILE *fp, int nlines, int maxline,
char *buf)
{
int m;
int me_universe = universe->me;
MPI_Comm uworld = universe->uworld;
if (me_universe == 0) {
m = 0;
for (int i = 0; i < nlines; i++) {
if (!fgets(&buf[m],maxline,fp)) {
m = 0;
break;
}
m += strlen(&buf[m]);
}
if (m) {
if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
m++;
}
}
MPI_Bcast(&m,1,MPI_INT,0,uworld);
if (m == 0) return 1;
MPI_Bcast(buf,m,MPI_CHAR,0,uworld);
return 0;
}

3
src/comm.h
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@ -114,9 +114,6 @@ class Comm : protected Pointers {
int (*)(int, char *, int &, int *&, char *&, void *),
int, char *&, int, void *, int statflag=0);
int read_lines_from_file(FILE *, int, int, char *);
int read_lines_from_file_universe(FILE *, int, int, char *);
// extract data useful to other classes
virtual void *extract(const char *, int &) {return nullptr;}

30
src/read_data.cpp
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@ -1226,7 +1226,7 @@ void ReadData::atoms()
while (nread < natoms) {
nchunk = MIN(natoms-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_atoms(nchunk,buffer,id_offset,mol_offset,toffset,shiftflag,shift);
nread += nchunk;
@ -1282,7 +1282,7 @@ void ReadData::velocities()
while (nread < natoms) {
nchunk = MIN(natoms-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_vels(nchunk,buffer,id_offset);
nread += nchunk;
@ -1324,7 +1324,7 @@ void ReadData::bonds(int firstpass)
while (nread < nbonds) {
nchunk = MIN(nbonds-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_bonds(nchunk,buffer,count,id_offset,boffset);
nread += nchunk;
@ -1398,7 +1398,7 @@ void ReadData::angles(int firstpass)
while (nread < nangles) {
nchunk = MIN(nangles-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_angles(nchunk,buffer,count,id_offset,aoffset);
nread += nchunk;
@ -1472,7 +1472,7 @@ void ReadData::dihedrals(int firstpass)
while (nread < ndihedrals) {
nchunk = MIN(ndihedrals-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_dihedrals(nchunk,buffer,count,id_offset,doffset);
nread += nchunk;
@ -1546,7 +1546,7 @@ void ReadData::impropers(int firstpass)
while (nread < nimpropers) {
nchunk = MIN(nimpropers-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_impropers(nchunk,buffer,count,id_offset,ioffset);
nread += nchunk;
@ -1613,7 +1613,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
while (nread < natoms) {
nchunk = MIN(natoms-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_bonus(nchunk,buffer,ptr,id_offset);
nread += nchunk;
@ -1739,7 +1739,7 @@ void ReadData::mass()
char *next;
char *buf = new char[ntypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf);
int eof = utils::read_lines_from_file(fp,ntypes,MAXLINE,buf,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
@ -1759,7 +1759,7 @@ void ReadData::paircoeffs()
char *next;
char *buf = new char[ntypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf);
int eof = utils::read_lines_from_file(fp,ntypes,MAXLINE,buf,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
@ -1785,7 +1785,7 @@ void ReadData::pairIJcoeffs()
int nsq = ntypes * (ntypes+1) / 2;
char *buf = new char[nsq * MAXLINE];
int eof = comm->read_lines_from_file(fp,nsq,MAXLINE,buf);
int eof = utils::read_lines_from_file(fp,nsq,MAXLINE,buf,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
@ -1811,7 +1811,7 @@ void ReadData::bondcoeffs()
char *next;
char *buf = new char[nbondtypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,nbondtypes,MAXLINE,buf);
int eof = utils::read_lines_from_file(fp,nbondtypes,MAXLINE,buf,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
@ -1836,7 +1836,7 @@ void ReadData::anglecoeffs(int which)
char *next;
char *buf = new char[nangletypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,nangletypes,MAXLINE,buf);
int eof = utils::read_lines_from_file(fp,nangletypes,MAXLINE,buf,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
@ -1862,7 +1862,7 @@ void ReadData::dihedralcoeffs(int which)
char *next;
char *buf = new char[ndihedraltypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf);
int eof = utils::read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
@ -1892,7 +1892,7 @@ void ReadData::impropercoeffs(int which)
char *next;
char *buf = new char[nimpropertypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,nimpropertypes,MAXLINE,buf);
int eof = utils::read_lines_from_file(fp,nimpropertypes,MAXLINE,buf,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
@ -1922,7 +1922,7 @@ void ReadData::fix(int ifix, char *keyword)
bigint nread = 0;
while (nread < nline) {
nchunk = MIN(nline-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) error->all(FLERR,"Unexpected end of data file");
modify->fix[ifix]->read_data_section(keyword,nchunk,buffer,id_offset);
nread += nchunk;

30
src/utils.cpp
View File

@ -225,6 +225,36 @@ void utils::sfread(const char *srcname, int srcline, void *s, size_t size,
/* ------------------------------------------------------------------ */
/* read N lines and broadcast */
int utils::read_lines_from_file(FILE *fp, int nlines, int nmax,
char *buffer, int me, MPI_Comm comm)
{
char *ptr = buffer;
*ptr = '\0';
if (me == 0) {
if (fp) {
for (int i = 0; i < nlines; i++) {
ptr = fgets(ptr,nmax,fp);
if (!ptr) break; // EOF?
// advance ptr to end of string and append newline char if needed.
ptr += strlen(ptr);
if (*(--ptr) != '\n') *(++ptr) = '\n';
// ensure buffer is null terminated. null char is start of next line.
*(++ptr) = '\0';
}
}
}
int n = strlen(buffer);
MPI_Bcast(&n,1,MPI_INT,0,comm);
if (n == 0) return 1;
MPI_Bcast(buffer,n+1,MPI_CHAR,0,comm);
return 0;
}
/* ------------------------------------------------------------------ */
std::string utils::check_packages_for_style(const std::string &style,
const std::string &name,
LAMMPS *lmp)

43
src/utils.h
View File

@ -17,9 +17,12 @@
/*! \file utils.h */
#include "lmptype.h"
#include <mpi.h>
#include <cstdio>
#include <string>
#include <vector>
#include <cstdio>
namespace LAMMPS_NS {
@ -52,7 +55,7 @@ namespace LAMMPS_NS {
void logmesg(LAMMPS *lmp, const std::string &mesg);
/** return a string representing the current system error status
/** Return a string representing the current system error status
*
* This is a wrapper around calling strerror(errno).
*
@ -60,8 +63,10 @@ namespace LAMMPS_NS {
std::string getsyserror();
/** safe wrapper around fgets() which aborts on errors
* or EOF and prints a suitable error message to help debugging
/** Safe wrapper around fgets() which aborts on errors
* or EOF and prints a suitable error message to help debugging.
*
* Use nullptr as the error parameter to avoid the abort on EOF or error.
*
* \param srcname name of the calling source file (from FLERR macro)
* \param srcline line in the calling source file (from FLERR macro)
@ -69,13 +74,15 @@ namespace LAMMPS_NS {
* \param size size of buffer s (max number of bytes read by fgets())
* \param fp file pointer used by fgets()
* \param filename file name associated with fp (may be a null pointer; then LAMMPS will try to detect)
* \param error pointer to Error class instance (for abort) */
* \param error pointer to Error class instance (for abort) or nullptr */
void sfgets(const char *srcname, int srcline, char *s, int size,
FILE *fp, const char *filename, Error *error);
/** safe wrapper around fread() which aborts on errors
* or EOF and prints a suitable error message to help debugging
/** Safe wrapper around fread() which aborts on errors
* or EOF and prints a suitable error message to help debugging.
*
* Use nullptr as the error parameter to avoid the abort on EOF or error.
*
* \param srcname name of the calling source file (from FLERR macro)
* \param srcline line in the calling source file (from FLERR macro)
@ -84,11 +91,31 @@ namespace LAMMPS_NS {
* \param num number of data elements read by fread()
* \param fp file pointer used by fread()
* \param filename file name associated with fp (may be a null pointer; then LAMMPS will try to detect)
* \param error pointer to Error class instance (for abort) */
* \param error pointer to Error class instance (for abort) or nullptr */
void sfread(const char *srcname, int srcline, void *s, size_t size,
size_t num, FILE *fp, const char *filename, Error *error);
/** Read N lines of text from file into buffer and broadcast them
*
* This function uses repeated calls to fread() to fill a buffer with
* newline terminated text. If a line does not end in a newline (e.g.
* at the end of a file), it is added. The caller has to allocate an
* nlines by nmax sized buffer for storing the text data.
* Reading is done by MPI rank 0 of the given communicator only, and
* thus only MPI rank 0 needs to provide a valid file pointer.
*
* \param fp file pointer used by fread
* \param nlines number of lines to be read
* \param nmax maximum length of a single line
* \param buffer buffer for storing the data.
* \param me MPI rank of calling process in MPI communicator
* \param comm MPI communicator for broadcast
* \return 1 if the read was short, 0 if read was successful */
int read_lines_from_file(FILE *fp, int nlines, int nmax,
char *buffer, int me, MPI_Comm comm);
/** Report if a requested style is in a package or may have a typo
*
* \param style type of style that is to be checked for

2
src/variable.cpp
View File

@ -5176,7 +5176,7 @@ int VarReader::read_peratom()
bigint nread = 0;
while (nread < nlines) {
nchunk = MIN(nlines-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) return 1;
char *buf = buffer;

34
unittest/formats/test_file_operations.cpp
View File

@ -11,13 +11,13 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "../testing/core.h"
#include "info.h"
#include "input.h"
#include "lammps.h"
#include "utils.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include "../testing/core.h"
#include <cstdio>
#include <mpi.h>
@ -28,6 +28,7 @@ using namespace LAMMPS_NS;
using testing::MatchesRegex;
using testing::StrEq;
using utils::read_lines_from_file;
using utils::sfgets;
using utils::sfread;
using utils::split_words;
@ -124,6 +125,37 @@ TEST_F(FileOperationsTest, safe_fread)
fclose(fp);
}
TEST_F(FileOperationsTest, read_lines_from_file)
{
char *buf = new char[MAX_BUF_SIZE];
FILE *fp = nullptr;
MPI_Comm world = MPI_COMM_WORLD;
int me, rv;
memset(buf, 0, MAX_BUF_SIZE);
rv = utils::read_lines_from_file(nullptr, 1, MAX_BUF_SIZE, buf, me, world);
ASSERT_EQ(rv, 1);
MPI_Comm_rank(world, &me);
if (me == 0) {
fp = fopen("safe_file_read_test.txt", "r");
ASSERT_NE(fp, nullptr);
} else
ASSERT_EQ(fp, nullptr);
rv = utils::read_lines_from_file(fp, 2, MAX_BUF_SIZE / 2, buf, me, world);
ASSERT_EQ(rv, 0);
ASSERT_THAT(buf, StrEq("one line\ntwo_lines\n"));
rv = utils::read_lines_from_file(fp, 2, MAX_BUF_SIZE / 2, buf, me, world);
ASSERT_EQ(rv, 0);
ASSERT_THAT(buf, StrEq("\nno newline\n"));
rv = utils::read_lines_from_file(fp, 2, MAX_BUF_SIZE / 2, buf, me, world);
ASSERT_EQ(rv, 1);
delete[] buf;
}
TEST_F(FileOperationsTest, logmesg)
{
char buf[8];