From fd404406e6b65d6d2e195ee91d693068e50fbff7 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Wed, 8 Jan 2014 10:10:57 +0100
Subject: [PATCH] Implementation of zlib
Files with gz extension are transparently compressed and decompressed.
Closes #17
---
src/config/Config.cpp.in | 9 ++++++
src/config/Config.h | 2 ++
src/core/CLToolMain.cpp | 2 ++
src/tools/FileBase.cpp | 57 +++++++++++++++++++++++----------
src/tools/FileBase.h | 8 ++++-
src/tools/IFile.cpp | 23 ++++++++++++--
src/tools/OFile.cpp | 68 +++++++++++++++++++++++++++++++++++++---
src/tools/OFile.h | 2 ++
8 files changed, 146 insertions(+), 25 deletions(-)
diff --git a/src/config/Config.cpp.in b/src/config/Config.cpp.in
index 4c326f277..5c850d41a 100644
--- a/src/config/Config.cpp.in
+++ b/src/config/Config.cpp.in
@@ -86,6 +86,15 @@ bool hasMolfile(){
#endif
}
+bool hasZlib(){
+#if __PLUMED_HAS_ZLIB
+ return true;
+#else
+ return false;
+#endif
+}
+
+
}
diff --git a/src/config/Config.h b/src/config/Config.h
index 81d7fc78b..c1f36f63f 100644
--- a/src/config/Config.h
+++ b/src/config/Config.h
@@ -45,6 +45,8 @@ bool hasCregex();
bool hasMolfile();
+bool hasZlib();
+
}
}
diff --git a/src/core/CLToolMain.cpp b/src/core/CLToolMain.cpp
index 1d2fa942c..790e04dfa 100644
--- a/src/core/CLToolMain.cpp
+++ b/src/core/CLToolMain.cpp
@@ -128,6 +128,8 @@ int CLToolMain::run(int argc, char **argv,FILE*in,FILE*out,Communicator& pc){
return (config::hasDlopen()?0:1);
} else if(a=="--has-molfile"){
return (config::hasMolfile()?0:1);
+ } else if(a=="--has-zlib"){
+ return (config::hasZlib()?0:1);
} else if(a=="--is-installed"){
return (config::isInstalled()?0:1);
} else if(a=="--no-mpi"){
diff --git a/src/tools/FileBase.cpp b/src/tools/FileBase.cpp
index 7dd31845e..0df6860be 100644
--- a/src/tools/FileBase.cpp
+++ b/src/tools/FileBase.cpp
@@ -32,6 +32,10 @@
#include <iostream>
#include <string>
+#ifdef __PLUMED_HAS_ZLIB
+#include <zlib.h>
+#endif
+
namespace PLMD{
void FileBase::test(){
@@ -69,11 +73,7 @@ FileBase& FileBase::link(FILE*fp){
}
FileBase& FileBase::flush(){
- fflush(fp);
- if(heavyFlush){
- fclose(fp);
- fp=std::fopen(const_cast<char*>(path.c_str()),"a");
- }
+ if(fp) fflush(fp);
return *this;
}
@@ -102,16 +102,17 @@ FileBase& FileBase::open(const std::string& path,const std::string& mode){
eof=false;
err=false;
fp=NULL;
- if(plumed){
- this->path=path+plumed->getSuffix();
- fp=std::fopen(const_cast<char*>(this->path.c_str()),const_cast<char*>(mode.c_str()));
- }
- if(!fp){
- this->path=path;
- fp=std::fopen(const_cast<char*>(this->path.c_str()),const_cast<char*>(mode.c_str()));
+ gzfp=NULL;
+ bool do_exist=FileExist(path);
+ fp=std::fopen(const_cast<char*>(this->path.c_str()),const_cast<char*>(mode.c_str()));
+ if(Tools::extension(this->path)=="gz"){
+#ifdef __PLUMED_HAS_ZLIB
+ gzfp=(void*)gzopen(const_cast<char*>(this->path.c_str()),const_cast<char*>(mode.c_str()));
+#else
+ plumed_merror("trying to use a gz file without zlib being linked");
+#endif
}
if(plumed) plumed->insertFile(*this);
- plumed_massert(fp,"file " + path + "cannot be found");
return *this;
}
@@ -120,7 +121,7 @@ bool FileBase::FileExist(const std::string& path){
FILE *ff=NULL;
bool do_exist=false;
if(plumed){
- this->path=path+plumed->getSuffix();
+ this->path=appendSuffix(path,plumed->getSuffix());
ff=std::fopen(const_cast<char*>(this->path.c_str()),"r");
}
if(!ff){
@@ -142,12 +143,17 @@ void FileBase::close(){
plumed_assert(!cloned);
eof=false;
err=false;
- std::fclose(fp);
+ if(fp) std::fclose(fp);
+#ifdef __PLUMED_HAS_ZLIB
+ if(gzfp) gzclose(gzFile(gzfp));
+#endif
fp=NULL;
+ gzfp=NULL;
}
FileBase::FileBase():
fp(NULL),
+ gzfp(NULL),
comm(NULL),
plumed(NULL),
action(NULL),
@@ -161,11 +167,30 @@ FileBase::FileBase():
FileBase::~FileBase()
{
if(plumed) plumed->eraseFile(*this);
- if(!cloned && fp) fclose(fp);
+ if(!cloned && fp) fclose(fp);
+#ifdef __PLUMED_HAS_ZLIB
+ if(!cloned && gzfp) gzclose(gzFile(gzfp));
+#endif
}
FileBase::operator bool()const{
return !eof;
}
+std::string FileBase::appendSuffix(const std::string&path,const std::string&suffix){
+ std::string ret=path;
+ std::string ext=Tools::extension(path);
+ if(ext=="gz"){
+ int l=path.length()-3;
+ plumed_assert(l>=0);
+ ret=ret.substr(0,l);
+ }
+ ret+=suffix;
+ if(ext=="gz")ret+=".gz";
+ return ret;
+}
+
+
+
+
}
diff --git a/src/tools/FileBase.h b/src/tools/FileBase.h
index 0ab890fe1..2cbd3b499 100644
--- a/src/tools/FileBase.h
+++ b/src/tools/FileBase.h
@@ -55,6 +55,8 @@ protected:
/// file pointer
FILE* fp;
+/// zip file pointer.
+ void* gzfp;
/// communicator. NULL if not set
Communicator* comm;
/// pointer to main plumed object. NULL if not linked
@@ -75,6 +77,10 @@ protected:
std::string path;
/// Set to true if you want flush to be heavy (close/reopen)
bool heavyFlush;
+/// Append suffix.
+/// It appends the desired suffix to the string. Notice that
+/// it conserves a possible ".gz" suffix.
+ static std::string appendSuffix(const std::string&path,const std::string&suffix);
public:
/// Link to an already open filed
FileBase& link(FILE*);
@@ -87,7 +93,7 @@ public:
/// Automatically links also the corresponding PlumedMain and Communicator.
FileBase& link(Action&);
/// Flushes the file to disk
- FileBase& flush();
+ virtual FileBase& flush();
/// Closes the file
/// Should be used only for explicitely opened files.
void close();
diff --git a/src/tools/IFile.cpp b/src/tools/IFile.cpp
index 00e9ca30b..fc95ecfe3 100644
--- a/src/tools/IFile.cpp
+++ b/src/tools/IFile.cpp
@@ -31,15 +31,29 @@
#include <iostream>
#include <string>
+#ifdef __PLUMED_HAS_ZLIB
+#include <zlib.h>
+#endif
namespace PLMD{
size_t IFile::llread(char*ptr,size_t s){
plumed_assert(fp);
size_t r;
- r=fread(ptr,1,s,fp);
- if(feof(fp)) eof=true;
- if(ferror(fp)) err=true;
+ if(gzfp){
+#ifdef __PLUMED_HAS_ZLIB
+ int rr=gzread(gzFile(gzfp),ptr,s);
+ if(rr==0) eof=true;
+ if(rr<0) err=true;
+ r=rr;
+#else
+ plumed_merror("trying to use a gz file without zlib being linked");
+#endif
+ } else {
+ r=fread(ptr,1,s,fp);
+ if(feof(fp)) eof=true;
+ if(ferror(fp)) err=true;
+ }
return r;
}
@@ -193,6 +207,9 @@ void IFile::reset(bool reset){
eof = reset;
err = reset;
if(!reset) clearerr(fp);
+#ifdef __PLUMED_HAS_ZLIB
+ if(!reset && gzfp) gzclearerr(gzFile(gzfp));
+#endif
return;
}
diff --git a/src/tools/OFile.cpp b/src/tools/OFile.cpp
index 55f6ac6a9..8d8ce53b3 100644
--- a/src/tools/OFile.cpp
+++ b/src/tools/OFile.cpp
@@ -34,6 +34,10 @@
#include <cstdlib>
#include <cerrno>
+#ifdef __PLUMED_HAS_ZLIB
+#include <zlib.h>
+#endif
+
namespace PLMD{
size_t OFile::llwrite(const char*ptr,size_t s){
@@ -41,7 +45,15 @@ size_t OFile::llwrite(const char*ptr,size_t s){
if(linked) return linked->llwrite(ptr,s);
if(! (comm && comm->Get_rank()>0)){
if(!fp) plumed_merror("writing on uninitilized File");
- r=fwrite(ptr,1,s,fp);
+ if(gzfp){
+#ifdef __PLUMED_HAS_ZLIB
+ r=gzwrite(gzFile(gzfp),ptr,s);
+#else
+ plumed_merror("trying to use a gz file without zlib being linked");
+#endif
+ } else {
+ r=fwrite(ptr,1,s,fp);
+ }
}
if(comm) comm->Bcast(r,0);
return r;
@@ -70,6 +82,7 @@ OFile::~OFile(){
OFile& OFile::link(OFile&l){
fp=NULL;
+ gzfp=NULL;
linked=&l;
return *this;
}
@@ -222,7 +235,7 @@ void OFile::setBackupString( const std::string& str ){
void OFile::backupAllFiles( const std::string& str ){
plumed_assert( backstring!="bck" && plumed && !plumed->getRestart() );
size_t found=str.find_last_of("/\\");
- std::string filename = str + plumed->getSuffix();
+ std::string filename = appendSuffix(str,plumed->getSuffix());
std::string directory=filename.substr(0,found+1);
std::string file=filename.substr(found+1);
if( FileExist(filename) ) backupFile("bck", filename);
@@ -266,16 +279,31 @@ OFile& OFile::open(const std::string&path){
eof=false;
err=false;
fp=NULL;
+ gzfp=NULL;
this->path=path;
if(plumed){
- this->path+=plumed->getSuffix();
+ this->path=appendSuffix(path,plumed->getSuffix());
}
if(plumed && plumed->getRestart()){
fp=std::fopen(const_cast<char*>(this->path.c_str()),"a");
+ if(Tools::extension(this->path)=="gz"){
+#ifdef __PLUMED_HAS_ZLIB
+ gzfp=(void*)gzopen(const_cast<char*>(this->path.c_str()),"a9");
+#else
+ plumed_merror("trying to use a gz file without zlib being linked");
+#endif
+ }
} else {
backupFile( backstring, this->path );
if(comm)comm->Barrier();
fp=std::fopen(const_cast<char*>(this->path.c_str()),"w");
+ if(Tools::extension(this->path)=="gz"){
+#ifdef __PLUMED_HAS_ZLIB
+ gzfp=(void*)gzopen(const_cast<char*>(this->path.c_str()),"w9");
+#else
+ plumed_merror("trying to use a gz file without zlib being linked");
+#endif
+ }
}
if(plumed) plumed->insertFile(*this);
return *this;
@@ -286,8 +314,38 @@ OFile& OFile::rewind(){
// the reason is that normal rewind does not work when in append mode
plumed_assert(fp);
clearFields();
- fclose(fp);
- fp=std::fopen(const_cast<char*>(path.c_str()),"w");
+ if(gzfp){
+#ifdef __PLUMED_HAS_ZLIB
+ gzclose((gzFile)gzfp);
+ gzfp=(void*)gzopen(const_cast<char*>(this->path.c_str()),"w9");
+#endif
+ } else {
+ fclose(fp);
+ fp=std::fopen(const_cast<char*>(path.c_str()),"w");
+ }
+ return *this;
+}
+
+FileBase& OFile::flush(){
+ if(heavyFlush){
+ if(gzfp){
+#ifdef __PLUMED_HAS_ZLIB
+ gzclose(gzFile(gzfp));
+ gzfp=(void*)gzopen(const_cast<char*>(path.c_str()),"a");
+#endif
+ } else{
+ fclose(fp);
+ fp=std::fopen(const_cast<char*>(path.c_str()),"a");
+ }
+ } else {
+ FileBase::flush();
+ // if(gzfp) gzflush(gzFile(gzfp),Z_FINISH);
+ // for some reason flushing with Z_FINISH has problems on linux
+ // I thus use this (incomplete) flush
+#ifdef __PLUMED_HAS_ZLIB
+ if(gzfp) gzflush(gzFile(gzfp),Z_FULL_FLUSH);
+#endif
+ }
return *this;
}
diff --git a/src/tools/OFile.h b/src/tools/OFile.h
index cad69614b..7ae4ffc0a 100644
--- a/src/tools/OFile.h
+++ b/src/tools/OFile.h
@@ -186,6 +186,8 @@ this method can be used to clean the field list.
friend OFile& operator<<(OFile&,const T &);
/// Rewind a file
OFile&rewind();
+/// Flush a file
+ virtual FileBase&flush();
};
/// Write using << syntax
--
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