File system compatibility

doc/source/faq.rst

@@ -39,6 +39,13 @@ The compilation stops while compiling Kokkos with ``/usr/include/stdlib.h(58): e
 When using the Intel compiler on a Mac Intel, I get a linking error involving the ``SharedAllocationRecordIvvE18t_tracking_enabledE`` symbol.
   This is a known bug of the Intel Mac compiler with Kokkos. Apparently Intel has decided not to fix it. Check the issue on the `Kokkos git page <https://github.com/kokkos/kokkos/issues/1959>`_.
 
+I get an error during *Idefix* link that says there are undefined symbols to std::filesystem
+  This is a known bug/limitation of the stdlibc++ provided with gcc8 that does not include C++17 filesystem extensions.
+  While *Idefix* auto-detects gcc8 when it is used as the main compiler, it still misses the cases when another compiler
+  (like Clang or Intel) is used with gcc8 as a backend.
+  You should try to clear up CMakeCache.txt and explicitely add the required link library when calling cmake as in
+  ``LDFLAGS=-lstdc++fs cmake $IDEFIX_DIR ...```
+
 Execution
 ---------
 

src/output/dump.cpp

@@ -6,7 +6,15 @@
 // ***********************************************************************************
 
 #include <unordered_set>
-#include <filesystem>
+#if __has_include(<filesystem>)
+  #include <filesystem>
+  namespace fs = std::filesystem;
+#elif __has_include(<experimental/filesystem>)
+  #include <experimental/filesystem>
+  namespace fs = std::experimental::filesystem;
+#else
+  error "Missing the <filesystem> header."
+#endif
 #include <iomanip>
 #include "dump.hpp"
 #include "version.hpp"
@@ -63,9 +71,9 @@ void Dump::Init(DataBlock *datain) {
   this->dumpFileNumber = 0;
 
   if(idfx::prank==0) {
-    if(!std::filesystem::is_directory(outputDirectory)) {
+    if(!fs::is_directory(outputDirectory)) {
       try {
-        if(!std::filesystem::create_directory(outputDirectory)) {
+        if(!fs::create_directory(outputDirectory)) {
           std::stringstream msg;
           msg << "Cannot create directory " << outputDirectory << std::endl;
           IDEFIX_ERROR(msg);
@@ -524,7 +532,7 @@ void Dump::ReadDistributed(IdfxFileHandler fileHdl, int ndim, int *dim, int *gdi
 // Helper function to convert filesystem::file_time into std::time_t
 // see https://stackoverflow.com/questions/56788745/
 // This conversion "hack" is required in C++17 as no proper conversion bewteen
-// std::filesystem::last_write_time and std::time_t
+// fs::last_write_time and std::time_t
 // exists in the standard library until C++20
 template <typename TP>
 std::time_t to_time_t(TP tp) {
@@ -533,15 +541,15 @@ std::time_t to_time_t(TP tp) {
     return std::chrono::system_clock::to_time_t(sctp);
 }
 
-int Dump::GetLastDumpInDirectory(std::filesystem::path &directory) {
+int Dump::GetLastDumpInDirectory(fs::path &directory) {
   int num = -1;
 
   std::time_t youngFileTime;
   bool first = true;
-  for (const auto & entry : std::filesystem::directory_iterator(directory)) {
+  for (const auto & entry : fs::directory_iterator(directory)) {
       // Check file extension
       if(entry.path().extension().string().compare(".dmp")==0) {
-        auto fileTime = to_time_t(std::filesystem::last_write_time(entry.path()));
+        auto fileTime = to_time_t(fs::last_write_time(entry.path()));
         // Check which one is the most recent
         if(first || fileTime>youngFileTime) {
           // std::tm *gmt = std::gmtime(&fileTime);
@@ -563,7 +571,7 @@ int Dump::GetLastDumpInDirectory(std::filesystem::path &directory) {
   return(num);
 }
 bool Dump::Read(Output& output, int readNumber ) {
-  std::filesystem::path filename;
+  fs::path filename;
   int nx[3];
   int nxglob[3];
   std::string fieldName;
@@ -574,7 +582,7 @@ bool Dump::Read(Output& output, int readNumber ) {
 
   idfx::pushRegion("Dump::Read");
 
-  std::filesystem::path readDir = this->outputDirectory;
+  fs::path readDir = this->outputDirectory;
 
   if(readNumber<0) {
     // We actually don't know which file we're supposed to read, so let's guess
@@ -746,7 +754,7 @@ bool Dump::Read(Output& output, int readNumber ) {
 
 
 int Dump::Write(Output& output) {
-  std::filesystem::path filename;
+  fs::path filename;
   char fieldName[NAMESIZE+1]; // +1 is just in case
   int nx[3];
   int nxtot[3];
@@ -776,8 +784,8 @@ int Dump::Write(Output& output) {
 
   // Check if file exists, if yes, delete it
   if(idfx::prank==0) {
-    if(std::filesystem::exists(filename)) {
-      std::filesystem::remove(filename);
+    if(fs::exists(filename)) {
+      fs::remove(filename);
     }
   }
 

src/output/dump.hpp

@@ -9,8 +9,15 @@
 #define OUTPUT_DUMP_HPP_
 #include <string>
 #include <map>
-#include <filesystem>
-
+#if __has_include(<filesystem>)
+  #include <filesystem>
+  namespace fs = std::filesystem;
+#elif __has_include(<experimental/filesystem>)
+  #include <experimental/filesystem>
+  namespace fs = std::experimental::filesystem;
+#else
+  error "Missing the <filesystem> header."
+#endif
 #include "idefix.hpp"
 #include "input.hpp"
 #include "dataBlock.hpp"
@@ -232,9 +239,9 @@ class Dump {
   void ReadSerial(IdfxFileHandler, int, int*, DataType, void*);
   void ReadDistributed(IdfxFileHandler, int, int*, int*, IdfxDataDescriptor&, void*);
   void Skip(IdfxFileHandler, int, int *, DataType);
-  int GetLastDumpInDirectory(std::filesystem::path &);
+  int GetLastDumpInDirectory(fs::path &);
 
-  std::filesystem::path outputDirectory;
+  fs::path outputDirectory;
 };
 
 

src/output/vtk.cpp

@@ -8,7 +8,15 @@
 #include <string>
 #include <sstream>
 #include <iomanip>
-#include <filesystem>
+#if __has_include(<filesystem>)
+  #include <filesystem>
+  namespace fs = std::filesystem;
+#elif __has_include(<experimental/filesystem>)
+  #include <experimental/filesystem>
+  namespace fs = std::experimental::filesystem;
+#else
+  error "Missing the <filesystem> header."
+#endif
 #include "vtk.hpp"
 #include "version.hpp"
 #include "idefix.hpp"
@@ -64,9 +72,9 @@ Vtk::Vtk(Input &input, DataBlock *datain, std::string filebase) {
   }
 
   if(idfx::prank==0) {
-    if(!std::filesystem::is_directory(outputDirectory)) {
+    if(!fs::is_directory(outputDirectory)) {
       try {
-        if(!std::filesystem::create_directory(outputDirectory)) {
+        if(!fs::create_directory(outputDirectory)) {
           std::stringstream msg;
           msg << "Cannot create directory " << outputDirectory << std::endl;
           IDEFIX_ERROR(msg);
@@ -247,7 +255,7 @@ int Vtk::Write() {
   idfx::pushRegion("Vtk::Write");
 
   IdfxFileHandler fileHdl;
-  std::filesystem::path filename;
+  fs::path filename;
 
   timer.reset();
 
@@ -260,8 +268,8 @@ int Vtk::Write() {
 
   // Check if file exists, if yes, delete it
   if(this->isRoot) {
-    if(std::filesystem::exists(filename)) {
-      std::filesystem::remove(filename);
+    if(fs::exists(filename)) {
+      fs::remove(filename);
     }
   }
 

src/output/vtk.hpp

@@ -9,7 +9,15 @@
 #define OUTPUT_VTK_HPP_
 #include <string>
 #include <map>
-#include <filesystem>
+#if __has_include(<filesystem>)
+  #include <filesystem>
+  namespace fs = std::filesystem;
+#elif __has_include(<experimental/filesystem>)
+  #include <experimental/filesystem>
+  namespace fs = std::experimental::filesystem;
+#else
+  error "Missing the <filesystem> header."
+#endif
 #include "idefix.hpp"
 #include "input.hpp"
 #include "dataBlock.hpp"
@@ -158,7 +166,7 @@ class Vtk : public BaseVtk {
   void WriteHeaderNodes(IdfxFileHandler);
 
   // output directory
-  std::filesystem::path outputDirectory;
+  fs::path outputDirectory;
 };
 
 template<typename T>