Merge pull request #126 in SAT/pbmm2 from bugfix/TAK-390-remove-max-mem-check to develop

* commit '754ee9c39678abca80f52e17c70f7d07b8bb3a7e':
  Do not check for max memory

Author: armintoepfer

meson.build

@@ -1,7 +1,7 @@
 project(
   'pbmm2',
   ['c', 'cpp'],
-  version : '1.2.0',
+  version : '1.2.1',
   default_options : [
     'buildtype=release',
     'warning_level=3',

src/AlignSettings.cpp

@@ -527,22 +527,6 @@ AlignSettings::AlignSettings(const PacBio::CLI_v2::Results& options)
                    << SortThreads << " threads for sorting, and " << maxMemSortFloat
                    << maxMemSortSuffix << " bytes RAM for sorting.";
 
-        auto pages = sysconf(_SC_PHYS_PAGES);
-        auto page_size = sysconf(_SC_PAGE_SIZE);
-        auto availableMemory = pages * page_size;
-
-        float availFloat;
-        std::string availSuffix;
-        MemoryToHumanReadable(availableMemory, &availFloat, &availSuffix);
-
-        if (maxMem > availableMemory) {
-            std::ostringstream os;
-            os << "Trying to allocate more memory for sorting (" << maxMemSortFloat
-               << maxMemSortSuffix << ") than system-wide available (" << availFloat << availSuffix
-               << ")";
-            throw AbortException(os.str());
-        }
-
         BamIdx = BamIndex::_from_string(bamIdx.c_str());
 
         if (noBai) {

tests/cram/baminput.t

@@ -360,10 +360,6 @@
   *Requested more threads for sorting* (glob)
   *Requested more threads for sorting* (glob)
 
-  $ $__PBTEST_PBMM2_EXE align $IN $REF $CRAMTMP/fail4.bam -j 1 -J 2 --sort -m 1000G 2>&1
-  *Trying to allocate more memory for sorting* (glob)
-  [1]
-
   $ $__PBTEST_PBMM2_EXE align $IN $REF $CRAMTMP/sort_percentage_4.bam -j 4 --sort --log-level INFO 2>&1 | grep "threads for alignments"
   *Using 3 threads for alignments, 1 threads for sorting, and 768M bytes RAM for sorting.* (glob)
 

tests/cram/misc.t

@@ -74,9 +74,6 @@
   $ $__PBTEST_PBMM2_EXE align $IN $REF $CRAMTMP/fail.bam --zmw --hqregion 2>&1; rm -rf $CRAMTMP/fail.bam
   *Options --zmw, --hqregion and --median-filter are mutually exclusive.* (glob)
 
-  $ $__PBTEST_PBMM2_EXE align $IN $REF $CRAMTMP/fail.bam --sort -J 1 -m 1000G 2>&1; rm -rf $CRAMTMP/fail.bam
-  *Trying to allocate more memory for sorting* (glob)
-
   $ $__PBTEST_PBMM2_EXE align $IN $REF $CRAMTMP/fail.bam --sort -J 1 -m 1000P 2>&1; rm -rf $CRAMTMP/fail.bam
   *Unknown size multiplier P* (glob)