pysharc compiles, but cannot read input files.

[diegoarmino]

Hi, everyone.

I've been dealing with a very slippery issue (at least to me). I compile pysharc as the manual indicates with a few modifications to the source/Makefile (apart from setting compiler and libs to gnu). The output of the command git diff source/Makefile is

$ git diff source/Makefile
diff --git a/source/Makefile b/source/Makefile
index 20b244f3..ad81917a 100644
--- a/source/Makefile
+++ b/source/Makefile
@@ -32,10 +32,10 @@
 USE_PYSHARC := true
 
 #intel, gnu
-USE_COMPILER := intel
+USE_COMPILER := gnu
 
 #mkl,gnu
-USE_LIBS := mkl
+USE_LIBS := gnu
 
 #Static libraries
 COMP_STATIC := false
@@ -79,8 +79,8 @@ ifeq ($(USE_COMPILER), )
   USE_COMPILER:=gnu
 endif
 ifeq ($(USE_COMPILER), gnu)
-  CC :=gcc
-  F90 :=gfortran 
+  CC :=$(CC)
+  F90 :=$(FC)
   EXTRAFLAGS := -ffree-line-length-none 
 else ifeq ($(USE_COMPILER), intel)
   CC:=icc

I set CC and F90 to the conda provided compilers. Also made the following changes to pysharc/netcdf/Makefile

diff --git a/pysharc/netcdf/Makefile b/pysharc/netcdf/Makefile
index 84e76e25..19d79b73 100644
--- a/pysharc/netcdf/Makefile
+++ b/pysharc/netcdf/Makefile
@@ -51,7 +51,7 @@ all: lib
 
 lib: $(OBJ_LIB)
        [ -d ../lib ] || mkdir ../lib
-       ar -cvq ../lib/$(library) $(OBJ_LIB)
+       $(AR) -cvq ../lib/$(library) $(OBJ_LIB)
 
 clean:
        rm ../lib/$(library)

In other words, I changed the hardcoded ar comand by $(AR) which corresponds to the conda provided version. All these changes avoided previous version mismatches between system, possible module loaded (lmod) and conda-provided compilers/libraries, in favor of the later ones.

The code compiled without errors, however when running tests 15 and 16 (LVC related) I run into a very confusing error. Sharc did not seem to be able to read the input file at all.

(sharc4.0) darmino@e03:/scratch/darmino/RUNNING_TESTS/LVC_pysharc$ cat output.log 

                                ,._gz,                                        ,._\
                               .g@@@p                                       ._Q@$+
                            ,.Q@@@@@f                                    ._Q@@@+  
                           .g@@@@@@@I                                 ._g@@@@F!   
                       ,,_zQ@@@@@@@@Q_,                            ,_zQ@@@@$+     
                .__ggQ@@@@@@@@@@@@@@@@@L_.              ,         _Q@@@@@@v       
       , __zg@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@QQz_z_zzQ@@L,    .zQ@@@@@@F`        
   .__gQ@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@Q\__zQ@@@@@@$+          
  G@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D            
    =4A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@$@@@@@L,           
        =vVAA@$@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@p=VX@@@B*   <V@$@@@Q_,         
                   @@@@@@@@@@P^^^^^^--`     -q@@$=`     =4V`       =X@@@@_        
                   1@@@@@@@$!                  ^`                       -`        
                   -q@@@@@@]                                                      
                    ($@@@@$`                                                      
                     4@@@@p                                                       
                      d@@@p                                                       
                       d@@b                                                       
                        =4!                                                       


 EXECUTION INFORMATION:
 Start date: Wed Feb 18 14:15:20 2026
 Run host: e03
 Run directory: /scratch/darmino/RUNNING_TESTS/LVC_pysharc

 BUILD INFORMATION:
 Build date: Wed Feb 18 13:41:02 -03 2026
 Build host: e03
 Build directory: /home/darmino/programas/sharc4-4.0.2/source
 Compiler: /home/darmino/miniconda3/envs/sharc4.0/bin/x86_64-conda-linux-gnu-gfortran
 PYSHARC activated: true

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<============================>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<   Program SHARC started    >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<============================>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

 Version: 4.0 (April 1, 2025)
 
 Print level:            2

 =============================================================
                          Input File
 =============================================================

 =============================================================
                             Restart
 =============================================================
 NO RESTART requested. Setting up the initial data from input files...

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<============================>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<   Initializing Dynamics    >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<============================>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
                                                                    Wed Feb 18 14:15:20 2026

Saving output data in NetCDF format (output.dat [header] + output.dat.nc)
Use data_extractor_NetCDF.x

 Keyword CHARGE not found.

After a long session of trial and error debugging, I managed to round up the problem to the subroutine read_input_list_from_file in the file source/input_list.f90. If I added a write statement like
write(,) "DEBUG: ", keyword, value
somewhere in the subroutine, the test ran successfully. However without it the error returned. It appears it is due to an optimization issue. If I turn off optimization for this file the problem fixes.
The complete set of changes I made to the code are summarized by the following git diff commands:

(sharc4.0) darmino@e03:~/programas/sharc4$ git diff source/Makefile
diff --git a/source/Makefile b/source/Makefile
index 20b244f3..ad81917a 100644
--- a/source/Makefile
+++ b/source/Makefile
@@ -32,10 +32,10 @@
 USE_PYSHARC := true
 
 #intel, gnu
-USE_COMPILER := intel
+USE_COMPILER := gnu
 
 #mkl,gnu
-USE_LIBS := mkl
+USE_LIBS := gnu
 
 #Static libraries
 COMP_STATIC := false
@@ -79,8 +79,8 @@ ifeq ($(USE_COMPILER), )
   USE_COMPILER:=gnu
 endif
 ifeq ($(USE_COMPILER), gnu)
-  CC :=gcc
-  F90 :=gfortran 
+  CC :=$(CC)
+  F90 :=$(FC)
   EXTRAFLAGS := -ffree-line-length-none 
 else ifeq ($(USE_COMPILER), intel)
   CC:=icc
@@ -122,6 +122,7 @@ CINCLUDE= -I$(ANACONDA)/include
 
 # flags
 F90FLAGS = -O3 -fPIC -g  $(EXTRAFLAGS)
+F90FLAGS_NOOPT = -O0 -fPIC -g  $(EXTRAFLAGS)
 
 # debug
 DEBUGFLAGS  = #-Wall -Wextra -Winline -Wno-unused-parameter -Wimplicit-interface -fbounds-check -fimplicit-none -fbacktrace -g 
@@ -309,7 +310,8 @@ clean:
 
 test_path:
        echo $(MAKEFILEPATH)
-
+input_list.o: input_list.f90
+       $(F90) $(FINCLUDE) $(DEBUGFLAGS) $(F90FLAGS_NOOPT) -c $<
 %.o: %.f90 
        $(F90) $(FINCLUDE) $(DEBUGFLAGS) $(F90FLAGS) -c $<
 
(sharc4.0) darmino@e03:~/programas/sharc4$ git diff source/input_list.f90
diff --git a/source/input_list.f90 b/source/input_list.f90
index b5000a90..802e19dc 100644
--- a/source/input_list.f90
+++ b/source/input_list.f90
@@ -56,12 +56,17 @@ private alloc_list, resize_list
     implicit none
     
     integer, intent(in) :: nunit
-    character*8000 :: keyword, value
+    character(len=8000) :: keyword, value
     integer :: io
     
     ! read all keywords into the variable size list and copy to output
     do 
       io=0 !no idea why something has to be here but without it the next line is not executed correctly
+
+      ! Initialize strings with spaces before use. This avoids garbage data or data from previous loops.
+      keyword = " "
+      value   = " "
+
       ! reads the next non-comment line from input file
       call next_keyword(nunit, keyword, value, io)
       if (io/=0) exit
(sharc4.0) darmino@e03:~/programas/sharc4$ git diff pysharc/netcdf/Makefile
diff --git a/pysharc/netcdf/Makefile b/pysharc/netcdf/Makefile
index 84e76e25..19d79b73 100644
--- a/pysharc/netcdf/Makefile
+++ b/pysharc/netcdf/Makefile
@@ -51,7 +51,7 @@ all: lib
 
 lib: $(OBJ_LIB)
        [ -d ../lib ] || mkdir ../lib
-       ar -cvq ../lib/$(library) $(OBJ_LIB)
+       $(AR) -cvq ../lib/$(library) $(OBJ_LIB)
 
 clean:
        rm ../lib/$(library)

[smausenberger]

Thats a known bug when compiling with gfortran.
#3 (comment)

[diegoarmino]

I didn't notice it. Sorry for the duplication. Should I comment in that thread instead and erase this one?