Fix ViennaRNA setup races and enable parallel accessibility folding

AGENTS.md

@@ -31,7 +31,7 @@ Apple Clang release on macOS.
 C++23 support is required in both the compiler and its standard library.
 `configure` checks `std::string::contains`, `std::string::resize_and_overwrite`
 and `std::stringstream::view`. Do not lower the language standard to work around
-an old toolchain. Dependencies include Boost, ViennaRNA (>= 2.4.14), zlib,
+an old toolchain. Dependencies include Boost, ViennaRNA (>= 2.7.0), zlib,
 pkg-config and Autotools; OpenMP is used by the default multithreaded build.
 [conda-build-env.yml](conda-build-env.yml) supplies library/build dependencies,
 but does not select the C++ compiler. Use the platform setup in CI when needed.
@@ -150,8 +150,15 @@ Example::isComplete() const
   comparison helpers from [general.h](src/IntaRNA/general.h). Internal energies
   use hundredths of kcal/mol; do not mix them with kcal/mol or Boltzmann values.
 - Preserve ownership and lifetimes when introducing RAII or non-owning views.
-  Retain synchronization around shared state and ViennaRNA calls; existing
-  accessibility calculations require serialization for thread safety.
+  Retain synchronization around shared ViennaRNA state: parameter/compound
+  setup, constraints and preparation use `VrnaHandler::getSetupMutex()`.
+  Prepared window accessibility computations can run concurrently with an
+  OpenMP-enabled ViennaRNA build; global MFE/PF calls remain serialized.
+  Complete parameter loading before workers start and preserve the mandatory
+  ViennaRNA logger lock. Retain full-call serialization for RNAlib builds
+  without OpenMP; this is a build-configuration boundary, not support for old
+  ViennaRNA releases. Consult `doc/analysis/vienna-accessibility-thread-safety.md`
+  before changing these boundaries.
 - For recurrence or predictor changes, extend the relevant regression tests
   and short-sequence oracles (`PredictorTinyOracle_test.cpp` and
   `PredictorSeedOracle_test.cpp`). For optimizations, compare correctness first,

ChangeLog

@@ -42,6 +42,15 @@
 
 ## Technical changes and Optimizations
 
+- require ViennaRNA >= 2.7.0 and its logger/prepared-window APIs at configure
+  time; install the logger lock for every supported version (PR #267)
+
+- fix ViennaRNA parameter-cache races and enable parallel prepared window
+  accessibility; retain serialization for global MFE/PF and non-OpenMP
+  ViennaRNA builds, with a source audit and concurrency regressions (issue #265)
+- keep the concurrency regression compatible with Apple Clang's standard
+  library using explicitly joined std::thread workers (PR #267)
+
 - add an API overview, IntaRNA Doxygen styling, and automated documentation
   builds and GitHub Pages publishing alongside the user guide (issue #22)
 
@@ -129,6 +138,48 @@ energies, restricted partition sums, and trackers.
 ################################################################################  
 ################################################################################
 
+261015 Alexander Mitrofanov
+ * configure.ac, conda-build-env.yml :
+   * require ViennaRNA >= 2.7.0, the first release with vrna_log_lock_set()
+   * check header version and link the logger/prepared-window APIs during
+     configure, including builds using --disable-pkg-config
+ * IntaRNA/VrnaHandler, IntaRNA/AccessibilityVrna :
+   * install the logger lock unconditionally for supported ViennaRNA releases
+     and remove obsolete version guards; retain full-call serialization for
+     RNAlib builds without OpenMP
+ * README.md, AGENTS.md, doc/analysis/vienna-accessibility-thread-safety.md :
+   * align the dependency and synchronization contract; distinguish historical
+     2.4.14 source evidence from the supported range and recorded runtime tests
+   + record minimum-version, release/debug and dependency-probe validation
+   * addresses review of https://github.com/BackofenLab/IntaRNA/pull/267
+
+261014 Alexander Mitrofanov
+ * tests/AccessibilityVrna_test.cpp :
+   * replace std::jthread, unavailable in the macOS CI standard library, with
+     std::thread and exception-safe joins before inspecting worker results
+   * fixes the Apple Clang regression build in PR #267
+ * tests/runAccessibilityThreads.sh :
+   * avoid empty-array expansion with nounset for older macOS Bash versions
+
+261014 Alexander Mitrofanov
+ * IntaRNA/VrnaHandler, IntaRNA/AccessibilityVrna,
+   IntaRNA/InteractionEnergyVrna, bin/IntaRNA :
+   * serialize shared parameter/compound setup, constraints and preparation
+     through one exception-safe mutex, including native-thread library callers
+   * run prepared window probability recurrences concurrently with OpenMP
+     ViennaRNA; retain the conservative fallback for other builds
+   * protect global MFE/PF compatibility state, remove worker-side global model
+     resets, and install a separate logger lock for ViennaRNA >= 2.7
+ * tests/AccessibilityVrna_test.cpp, tests/runAccessibilityThreads.sh,
+   tests/Makefile.am :
+   + compare serial/native-thread/OpenMP ED, ES and ensemble energies with
+     varied models; compare CLI accessibilities/predictions with SHAPE D/W
+ * doc/analysis/vienna-accessibility-thread-safety.md,
+   doc/analysis/vrna-window-threads.cpp, doc/Makefile.am, README.md, AGENTS.md :
+   + trace IntaRNA and ViennaRNA shared/owned state, provide an independent
+     race reproducer and document supported concurrency boundaries
+   * resolves https://github.com/BackofenLab/IntaRNA/issues/265
+
 261007 Alexander Mitrofanov
  * doc/doxygen.cfg, doc/doxygen/* :
    + introduce the API main page with component links, prediction flow,

README.md

@@ -194,7 +194,10 @@ dependencies:
     - libboost_system
     - libboost_iostreams
     - libboost_serialization
-- [Vienna RNA package](http://www.tbi.univie.ac.at/RNA/) version >= 2.4.14
+- [Vienna RNA package](http://www.tbi.univie.ac.at/RNA/) version >= 2.7.0,
+  providing the logger locking API required for concurrent accessibility
+  calculations. Configure checks the version and required APIs, including
+  when `--disable-pkg-config` is used.
 - `pkg-config` for detailed version checks of dependencies
 - if [cloning from github](#instgithub): GNU autotools (automake, autoconf, ..)
 
@@ -457,6 +460,16 @@ The maximal number of threads to be used can be specified using the `--threads`
 If `--threads=k != 1`, than *k* predictions are processed in parallel. A value of
 `0` requests the maximally available number of threads for this machine.
 
+ViennaRNA accessibility calculations for independent sequences run concurrently
+when ViennaRNA was built with OpenMP support. IntaRNA serializes parameter and
+constraint setup to protect ViennaRNA's shared caches; builds without ViennaRNA
+OpenMP support retain serial accessibility calculation. IntaRNA installs a
+separate ViennaRNA logger lock during handler initialization for every
+supported version. Global intramolecular MFE/partition-function calls remain
+serialized. See the
+[thread-safety audit](doc/analysis/vienna-accessibility-thread-safety.md) for the
+call sequence, source evidence, standalone reproducer and validation.
+
 When using parallelization, you should have the following in mind:
 
 - The memory consumption will be multiplied by the number of threads,

conda-build-env.yml

@@ -12,7 +12,7 @@ dependencies:
   - pkgconfig
   - zlib
   - boost-cpp
-  - viennarna>=2.4.14
+  - viennarna>=2.7.0
   - cxx-compiler
   - make
   - binutils

configure.ac

@@ -5,8 +5,8 @@ AC_INIT([IntaRNA], [3.4.1], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
 
 # minimal required version of the boost library 
 BOOST_REQUIRED_VERSION=1.50.0
-# minimal required version of the Vienna RNA library
-VRNA_REQUIRED_VERSION=2.4.14
+# minimal Vienna RNA version providing the logger locking API
+VRNA_REQUIRED_VERSION=2.7.0
 # minimal required version of python interpreter (to install intarnapvalue)
 PYTHON_REQUIRED_VERSION=3.6
 
@@ -443,19 +443,41 @@ AS_IF([test x"$HAVE_PKG_CONFIG" = x"yes"], [
 ])
 
 AS_IF([test "$RNANOTFOUND" = "0"], [
-	AC_MSG_CHECKING([for compilation with Vienna RNA package headers])
+	AC_MSG_CHECKING([for ViennaRNA >= $VRNA_REQUIRED_VERSION with logger locking and prepared window folding])
 	OLD_CPPFLAGS=$CPPFLAGS
-	OLD_CXXFLAGS=$CXXFLAGS
 	OLD_LDFLAGS=$LDFLAGS
-	AC_LANG_PUSH([C])
+	intarna_saved_vrna_LIBS=$LIBS
+	AC_LANG_PUSH([C++])
 	CPPFLAGS="$CPPFLAGS $AM_CXXFLAGS"
 	LDFLAGS="$LDFLAGS $AM_LDFLAGS"
 	AS_IF([test "x$HAVE_PKG_CONFIG" = "xyes"], [
 		CPPFLAGS="$CPPFLAGS $VRNA_CFLAGS"
-		LDFLAGS="$LDFLAGS $VRNA_LIBS"
+		LIBS="$VRNA_LIBS $LIBS"
+	], [
+		LIBS="-lRNA $LIBS"
 	])
-	AC_COMPILE_IFELSE(
-	     [AC_LANG_PROGRAM([[#include <ViennaRNA/model.h>]],[[vrna_md_t tmp; vrna_md_copy(&tmp,&tmp);]])],
+	# Check headers even without pkg-config, and link the APIs used for concurrency.
+	AC_LINK_IFELSE(
+	     [AC_LANG_PROGRAM([[
+extern "C" {
+#include <ViennaRNA/vrna_config.h>
+#if VRNA_VERSION_MAJOR < 2 || (VRNA_VERSION_MAJOR == 2 && VRNA_VERSION_MINOR < 7)
+#error ViennaRNA 2.7.0 or newer is required
+#endif
+#include <ViennaRNA/model.h>
+#include <ViennaRNA/fold_compound.h>
+#include <ViennaRNA/partfunc/local.h>
+#include <ViennaRNA/utils/log.h>
+}
+]], [[
+vrna_md_t model;
+vrna_md_set_default(&model);
+vrna_log_lock_set(NULL, NULL);
+vrna_fold_compound_t *fc = vrna_fold_compound("GCGC", &model, VRNA_OPTION_PF | VRNA_OPTION_WINDOW);
+vrna_fold_compound_prepare(fc, VRNA_OPTION_PF | VRNA_OPTION_WINDOW);
+vrna_probs_window(fc, 4, VRNA_PROBS_WINDOW_UP, NULL, NULL);
+vrna_fold_compound_free(fc);
+]])],
 	     [ 
 			AC_MSG_RESULT([yes])
 			RNANOTFOUND=0;
@@ -467,9 +489,10 @@ AS_IF([test "$RNANOTFOUND" = "0"], [
 	       RNANOTFOUND=1;
 	     ]
 	)
-	AC_LANG_POP([C])
+	AC_LANG_POP([C++])
 	CPPFLAGS=$OLD_CPPFLAGS
 	LDFLAGS=$OLD_LDFLAGS
+	LIBS=$intarna_saved_vrna_LIBS
 ])
 
 # error output if ViennaRNA not found