Improve doc of parallelism, as well as output in log files

doc/guide/abinit.md

@@ -1231,6 +1231,7 @@ information on such files:
   * [[prtgeo]] to print a file with a geometrical analysis (bond lengths and bond angles), that also contains an XMOL section
   * [[prt1dm]] to print a one-dimensional projection of potential and density, for the three axes.
 
+<a id="control-of-output-in-the-parallel-case"></a>
 ### 5.9 Control of output in the parallel case
   
 For massively parallel runs, one cannot afford to have some of the output

doc/topics/_parallelism.md

@@ -21,8 +21,11 @@ export OMP_NUM_THREADS=4
 mpirun -n 10 abinit run.abi > log 2> err   
 ```
 
-In the latter, the standard output of the application is redirected to `log` while `err` collects the standard error.
 The command *mpirun* might possibly be replaced by *mpiexec* depending on your system.
+In the latter, the standard output of the application is redirected to `log` while `err` collects the standard error.
+Note that the control of output in the parallel case needs to be adapted, as for massively parallel runs, 
+one cannot afford to have some of the output files that are usually created, see 
+the [[help:abinit#control-of-output-in-the-parallel-cas|abinit help file]] for more explanation and how to change the default behavior (_LOG/_NOLOG files).
 
 * For ground-state calculations, the code has been parallelized (MPI-based parallelism) 
   on the k-points, the spins, the spinor components, the bands, and the FFT grid and plane wave coefficients. 

doc/tutorial/basepar.md

@@ -213,7 +213,7 @@ to a local temporary disk space named `/scratch/user`, then you might add to the
 Note that determining ahead of time the precise resources you will need for
 your run will save you a lot of time if you are using a batch queue system.
 
-Also, for parallel runs, note that the _log_ files **will not** be written exept the main log file.
+Also, for parallel runs, note that the _log_ files **will not** be written except the main log file.
 You can change this behaviour by creating a file named `_LOG` to enforce the creation of all log files
 
 ```bash

src/44_abitypes_defs/m_dtfil.F90

@@ -1509,7 +1509,8 @@ end subroutine isfile
 !! iofn1
 !!
 !! FUNCTION
-!! Begin by eventual redefinition of unit std_in and std_out
+!! Define values of do_write_log and do_write_status parameters
+!! Eventual redefinition of unit std_in and std_out
 !! Then, print greetings for interactive user.
 !! Next, read filenames from unit std_in, AND check that new
 !! output file does not already exist.
@@ -1557,10 +1558,10 @@ subroutine iofn1(input_path, filnam, filstat, comm)
  real(dp),allocatable :: dprarr(:)
 !*************************************************************************
 
- ! NOTE: In this routine it's very important to perform tests
+ ! NOTE: In this routine it is very important to perform tests
  ! on possible IO errors (err=10, iomsg) because we are initializing the IO stuff
- ! It there's some problem with the hardware or some misconfiguration,
- ! it's very likely that the code will crash here and we should try to give useful error messages.
+ ! If there is some problem with the hardware or some misconfiguration,
+ ! it is very likely that the code will crash here and we should try to give useful error messages.
 
  blank = ' '; tmpfil = ''
 
@@ -1768,6 +1769,10 @@ subroutine iofn1(input_path, filnam, filstat, comm)
      if (open_file(fillog,msg,unit=std_out,status='unknown',action="write") /= 0) then
        ABI_ERROR(msg)
      end if
+!    Print greetings for interactive user
+     write(std_out,*,err=10,iomsg=errmsg)' ABINIT ',trim(abinit_version)
+     write(std_out,*,err=10,iomsg=errmsg)' '
+     write(std_out,*,err=10,iomsg=errmsg)' I am not the master. Writing log in ',fillog 
    else
      close(std_out, err=10, iomsg=errmsg)
      if (open_file(NULL_FILE,msg,unit=std_out,action="write") /= 0) then

src/51_manage_mpi/m_wffile.F90

@@ -2641,7 +2641,7 @@ subroutine xderiveRead_int2d_displ(wff,xval,n1,n2,spaceComm,displace,ierr)
      depl_val(ipos)=ipos
    end do
  end do
-!To save time, the location describe by array map must be in increasing order
+!To save time, the location described by array map must be in increasing order
  nbval=0
  do i1=0,totsize-1
    if (depl_val(i1)/=-1) then

src/98_main/abinit.F90

@@ -254,6 +254,9 @@ program abinit
    call wrtout([std_out, ab_out], msg)
  end if
 
+ msg=' abinit : after writing the name of files '
+ call wrtout(std_out,msg,'PERS')
+
  ! Test if the netcdf library supports MPI-IO
  call nctk_test_mpiio()