merged ejh_bug_fix branch

.travis.yml

@@ -2,6 +2,10 @@ language: c
 dist: trusty
 sudo: false
 
+branches:
+  only:
+  - master
+
 addons:
   apt:
     sources:
@@ -17,17 +21,34 @@ before_install:
 
 before_script:
   - export CC=mpicc
+  - export FC=mpif90
   - export CPPFLAGS='-I/usr/include'
-
+  - wget https://parallel-netcdf.github.io/Release/pnetcdf-1.11.0.tar.gz 
+  - tar -xzvf pnetcdf-1.11.0.tar.gz
+  - ls -l
+  - pushd pnetcdf-1.11.0
+  - ./configure --prefix=/usr --enable-shared
+  - make
+  - sudo make install
+  - popd
 env:
   global:
     - CC=mpicc
+    - FC=mpif90
     - CPPFLAGS='-I/usr/include'
     - CFLAGS='-std=c99'
     - LDFLAGS='-L/usr/lib'
 
 script:
   - autoreconf -i
+  - export CFLAGS='-std=c99  -fsanitize=address -fno-omit-frame-pointer'
   - ./configure
   - make -j distcheck
-
+  - export CFLAGS='-std=c99'
+  - rm -rf build
+  - mkdir build
+  - cd build
+  - cmake -DPIO_HDF5_LOGGING=On -DPIO_USE_MALLOC=On -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off ..
+  - make VERBOSE=1
+  - make tests VERBOSE=1
+  - make test VERBOSE=1

README.md

@@ -4,7 +4,8 @@ A high-level Parallel I/O Library for structured grid applications
 
 ## Website
 
-For complete documentation, see our website at [http://ncar.github.io/ParallelIO/](http://ncar.github.io/ParallelIO/).
+For complete documentation, see our website at
+[http://ncar.github.io/ParallelIO/](http://ncar.github.io/ParallelIO/).
 
 ## Mailing List
 

configure.ac

@@ -41,6 +41,7 @@ if test "x$enable_logging" = xyes; then
    AC_DEFINE([PIO_ENABLE_LOGGING], 1, [If true, turn on logging.])
 fi
 
+
 # Does the user want to enable Fortran library?
 AC_MSG_CHECKING([whether Fortran library should be build])
 AC_ARG_ENABLE([fortran],
@@ -50,6 +51,17 @@ test "x$enable_fortran" = xyes || enable_fortran=no
 AC_MSG_RESULT([$enable_fortran])
 AM_CONDITIONAL(BUILD_FORTRAN, [test "x$enable_fortran" = xyes])
 
+# Does the user want to disable pnetcdf?
+AC_MSG_CHECKING([whether pnetcdf is to be used])
+AC_ARG_ENABLE([pnetcdf],
+              [AS_HELP_STRING([--disable-pnetcdf],
+                              [Disable pnetcdf use.])])
+test "x$enable_pnetcdf" = xno || enable_pnetcdf=yes
+AC_MSG_RESULT([$enable_pnetcdf])
+if test "x$enable_logging" = xyes; then
+   AC_DEFINE([PIO_ENABLE_LOGGING], 1, [If true, turn on logging.])
+fi
+
 # NetCDF (at least classic) is required for PIO to build.
 AC_DEFINE([_NETCDF], [1], [netCDF classic library available])
 
@@ -75,6 +87,9 @@ AC_CHECK_LIB([netcdf], [nc_create], [], [AC_MSG_ERROR([Can't find or link to the
 
 # Check for pnetcdf library.
 AC_CHECK_LIB([pnetcdf], [ncmpi_create], [], [])
+if test "x$ac_cv_lib_pnetcdf_ncmpi_create" = xno -a $enable_pnetcdf = yes; then
+   AC_MSG_ERROR([Pnetcdf not found. Set CPPFLAGS/LDFLAGS or use --disable-pnetcdf.])
+fi
 
 # If we have parallel-netcdf, then set these as well.
 if test x$ac_cv_lib_pnetcdf_ncmpi_create = xyes; then

examples/c/run_tests.sh

@@ -1,11 +1,12 @@
+#!/bin/sh
 # This is a test script for PIO examples.
 # Ed Hartnett 5/7/18
 
 # Stop execution of script if error is returned.
 set -e
 
 # Stop loop if ctrl-c is pressed.
-trap exit SIGINT SIGTERM
+trap exit INT TERM
 
 printf 'running PIO examples...\n'
 

src/clib/pio_getput_int.c

@@ -866,8 +866,14 @@ int PIOc_get_var_tc(int ncid, int varid, nc_type xtype, void *buf)
 
         /* Find the dimension lengths. */
         for (int d = 0; d < ndims; d++)
+        {
             if ((ierr = PIOc_inq_dimlen(ncid, dimids[d], &countp[d])))
+            {
+                free(startp);
+                free(countp);
                 return pio_err(ios, file, ierr, __FILE__, __LINE__);
+            }
+        }
 
         /* Set up start array. */
         for (int d = 0; d < ndims; d++)

src/clib/pio_msg.c

@@ -1225,9 +1225,9 @@ int inq_var_deflate_handler(iosystem_desc_t *ios)
     char shuffle_present;
     char deflate_present;
     char deflate_level_present;
-    int shuffle, *shufflep;
-    int deflate, *deflatep;
-    int deflate_level, *deflate_levelp;
+    int shuffle, *shufflep = NULL;
+    int deflate, *deflatep = NULL;
+    int deflate_level, *deflate_levelp = NULL;
     int mpierr;
 
     assert(ios);
@@ -2331,9 +2331,9 @@ int get_chunk_cache_handler(iosystem_desc_t *ios)
     int iosysid;
     int iotype;
     char size_present, nelems_present, preemption_present;
-    PIO_Offset size, *sizep;
-    PIO_Offset nelems, *nelemsp;
-    float preemption, *preemptionp;
+    PIO_Offset size, *sizep = NULL;
+    PIO_Offset nelems, *nelemsp = NULL;
+    float preemption, *preemptionp = NULL;
     int mpierr = MPI_SUCCESS;  /* Return code from MPI function codes. */
 
     LOG((1, "get_chunk_cache_handler called"));
@@ -2384,9 +2384,9 @@ int get_var_chunk_cache_handler(iosystem_desc_t *ios)
     int ncid;
     int varid;
     char size_present, nelems_present, preemption_present;
-    PIO_Offset size, *sizep;
-    PIO_Offset nelems, *nelemsp;
-    float preemption, *preemptionp;
+    PIO_Offset size, *sizep = NULL;
+    PIO_Offset nelems, *nelemsp = NULL;
+    float preemption, *preemptionp = NULL;
     int mpierr = MPI_SUCCESS;  /* Return code from MPI function codes. */
 
     LOG((1, "get_var_chunk_cache_handler called"));

src/clib/pio_rearrange.c

@@ -2076,7 +2076,6 @@ void performance_tune_rearranger(iosystem_desc_t *ios, io_desc_t *iodesc)
     if (!(wall = bget(2 * 4 * log2 * sizeof(double))))
         return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
     double mintime;
-    int k = 0;
 
     if ((mpierr = MPI_Barrier(mycomm)))
         return check_mpi(NULL, mpierr, __FILE__, __LINE__);

src/clib/pioc_support.c

@@ -880,8 +880,8 @@ int PIOc_readmap(const char *file, int *ndims, int **gdims, PIO_Offset *fmaplen,
         if (!fp)
             pio_err(NULL, NULL, PIO_EINVAL, __FILE__, __LINE__);
 
-        fscanf(fp,"version %d npes %d ndims %d\n",&rversno, &rnpes, ndims);
-
+        if (fscanf(fp,"version %d npes %d ndims %d\n", &rversno, &rnpes, ndims) != 3)
+            pio_err(NULL, NULL, PIO_EINVAL, __FILE__, __LINE__);
         if (rversno != VERSNO)
             return pio_err(NULL, NULL, PIO_EINVAL, __FILE__, __LINE__);
 
@@ -895,20 +895,23 @@ int PIOc_readmap(const char *file, int *ndims, int **gdims, PIO_Offset *fmaplen,
         if (!(tdims = calloc(*ndims, sizeof(int))))
             return pio_err(NULL, NULL, PIO_ENOMEM, __FILE__, __LINE__);
         for (int i = 0; i < *ndims; i++)
-            fscanf(fp,"%d ", tdims + i);
+            if (fscanf(fp,"%d ", tdims + i) != 1)
+                pio_err(NULL, NULL, PIO_EINVAL, __FILE__, __LINE__);
 
         if ((mpierr = MPI_Bcast(tdims, *ndims, MPI_INT, 0, comm)))
             return check_mpi(NULL, mpierr, __FILE__, __LINE__);
 
         for (int i = 0; i < rnpes; i++)
         {
-            fscanf(fp, "%d %lld", &j, &maplen);
+            if (fscanf(fp, "%d %lld", &j, &maplen) != 2)
+                pio_err(NULL, NULL, PIO_EINVAL, __FILE__, __LINE__);
             if (j != i)  // Not sure how this could be possible
                 return pio_err(NULL, NULL, PIO_EINVAL, __FILE__, __LINE__);
             if (!(tmap = malloc(maplen * sizeof(PIO_Offset))))
                 return pio_err(NULL, NULL, PIO_ENOMEM, __FILE__, __LINE__);
             for (j = 0; j < maplen; j++)
-                fscanf(fp, "%lld ", tmap+j);
+                if (fscanf(fp, "%lld ", tmap + j) != 1)
+                    pio_err(NULL, NULL, PIO_EINVAL, __FILE__, __LINE__);
 
             if (i > 0)
             {

tests/cunit/Makefile.am

@@ -19,7 +19,7 @@ test_darray_multivar3 test_darray_1d test_darray_3d			\
 test_decomp_uneven test_decomps test_rearr test_darray_async_simple	\
 test_darray_async test_darray_async_many test_darray_2sync		\
 test_async_multicomp test_async_multi2 test_async_manyproc		\
-test_darray_fill test_decomp_frame test_perf1 test_perf2
+test_darray_fill test_decomp_frame test_perf2
 
 # Tests will run from a bash script.
 TESTS = run_tests.sh
@@ -59,7 +59,6 @@ test_async_multi2_SOURCES = test_async_multi2.c test_common.c pio_tests.h
 test_async_manyproc_SOURCES = test_async_manyproc.c test_common.c pio_tests.h
 test_darray_fill_SOURCES = test_darray_fill.c test_common.c pio_tests.h
 test_decomp_frame_SOURCES = test_decomp_frame.c test_common.c pio_tests.h
-test_perf1_SOURCES = test_perf1.c test_common.c pio_tests.h
 test_perf2_SOURCES = test_perf2.c test_common.c pio_tests.h
 
 # Distribute the test script.

tests/cunit/pio_tests.h

@@ -77,6 +77,14 @@
         return e;                                                       \
     } while (0)
 
+/** Handle non-MPI errors by finalizing the MPI library and goto
+ * exit. */
+#define BAIL(e) do {                                                     \
+        fprintf(stderr, "%d Error %d in %s, line %d\n", my_rank, e, __FILE__, __LINE__); \
+        MPI_Finalize();                                                 \
+        goto exit;                                                      \
+    } while (0)
+
 /** Global err buffer for MPI. When there is an MPI error, this buffer
  * is used to store the error message that is associated with the MPI
  * error. */

tests/cunit/run_tests.sh

@@ -1,11 +1,12 @@
+#!/bin/sh
 # This is a test script for PIO.
 # Ed Hartnett
 
 # Stop execution of script if error is returned.
 set -e
 
 # Stop loop if ctrl-c is pressed.
-trap exit SIGINT SIGTERM
+trap exit INT TERM
 
 printf 'running PIO tests...\n'