gentoo resync : 14.05.2020

6 files changed, 57 insertions, 64 deletions

diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index 126511a8fbea..63bf7503661c 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,9 +1,9 @@
-AUX petsc-3.12.1-do_not_run_mpiexec.patch 2648 BLAKE2B 521db3b12644ec692134f11e96d2ec633f3600199e2ac4da5cf2ee6be566fc6e65d0b6a67437752b0c1cf656561ba6c991d2ad603d3975f334b66362d275483c SHA512 b5eb5406203ae4df21d94755f8ccb996c7d6822ef93a60ebe3a82f404436f1aa314809f63bbcbdc15a5613ff143df80e3e69b3e3f48dc9521a2e2855dad73e25
-AUX petsc-3.12.1-make_hypre_configure.patch 3970 BLAKE2B 562cab7e3176acf2bce1b40d4a8563718d419be95881b7fb68fee563591db8bc9fac7444885139c9887e3ab8fe790c4568dbc58cff43f718dbace335564ec1fb SHA512 7f954e6a9a2e3eabe15c9eca6dd385a6a50a5cb7dcda8fd0de8fa2ff49667850fcad62a3b3caade0bc024a1eef1bf4f1f429385e9208b95badb77d814480357c
+AUX petsc-3.13.0-do_not_run_mpiexec.patch 2822 BLAKE2B 6c8e8185c693fdc720c0d8ea803cecff2d4b29ae71e3251e06e3460e05b301b709f30032f9a473f065c3e2a9a7b488241cb0d63ddaebdcdf275513af50257ddc SHA512 c2ea68fd59feed34ea6b7afdcbfe24e27e44d844ed6f077c52b81a20676dabb4613c9add6b33edea7d46f0c1a55993bd020d342092aa15e0f46020cc6bc51609
+AUX petsc-3.13.0-fix_sandbox_violation.patch 1022 BLAKE2B 4883be2a38becba88dd1ceafffae46b775f75a59ce990c2d92808a52fb27e5ab89a14e355599009466be0af58680076e15ae74d82cd243b3bfe867fa90f4f05a SHA512 afd6e4ade2a53941d0211baa78e179de9c8bfead15c4c245d25623cee99fb1c0821d154e58428b3c431654d770689afdec1c2bd631f2fa8eedd99d3c7186656c
+AUX petsc-3.13.0-make_hypre_configure.patch 4055 BLAKE2B e3bc831665fbe2c9a724a13420d1ce7557b7a1a6fcd7537271a6e48622f29f71f72257d649bcbef4aa4f287a804407cdb80579797eb54cfa994ef85d5bcb617f SHA512 47e4971596342c160fc54e1bc6d9fa739ae4bf6a9e3f89659992a3548de0beacdc7ac34a900117c1ee43b6bfaa81e8a58f1c45acea072be612ece3b5d18d7f86
 AUX petsc-3.7.0-disable-rpath.patch 909 BLAKE2B b9b6064886d6c10b382982778398cb7fa254242e5ed0dfb86dd4cd6c094dc51eecfd625f6de5c2779bfc5b3beda351ac44145c69ac246d814a728d7565da8086 SHA512 8241c593d903615feb175bfe8213792ace739a18ac5f4c1d1890155ccea7de30b5ef5d97e2fa3b043e9a1e520e022abedeb038d0b4db671f89045e04edc65a68
-AUX petsc-3.9.0-fix_sandbox_violation.patch 916 BLAKE2B f58ba79c3082d253c9a95b0c9ce0bcc6373fa91b4155fac5a6d4688c21805d938f5c04a939ab9d8b810732e79699e7156bd4916717b9ab0217ab257ca64bb92e SHA512 cde22a54f0f6c73cfa326ea0c0026878b3099381ec703154bb8d2746a502ffc9ae82e65082f63579abce5b3d3f89bccf0cbc7db7d031e642c5c02ca8281e616c
-DIST petsc-3.11.3.tar.gz 33279017 BLAKE2B 870b8245e5e06d8538ea3ee1d01fa2cebade4a0bd79dfcf17d74e6201f41d21ca021e206744ece28847b434ece142a2789851b5514a8a1e3f82a8551288b695b SHA512 e545f69e87bc72950939ff3cec3e0ba225a5b3e7f1cb93b0fb6123194eb7240ac1d97ba397235d8ab872c653caab1427673124e5e1e706b796c0ae46ec1bcffa
-DIST petsc-3.12.1.tar.gz 34592587 BLAKE2B b48056a1fe1d507338f7d145f5fceeab2b2f576470d8af90c9d7828de9b775daadf11198fecc46b5e48fcf1eb38addb366e3a908dab5c4ffaf7f9b71ff17b3d8 SHA512 df33170922c0b34136d2fd5bdc3c68a80d3a5873d66bfb03b2cea4a6456393c7181a8da673911b89ea0fcb51d5fd89b5b4c8b76ddb1df573180a92d029fbc1fb
-EBUILD petsc-3.11.3.ebuild 5337 BLAKE2B bdd7062ad5b5b55de97c676a30437901838749d9ee910d274711668de7b43d1f0c630b53e1f4f0b50442ea05b3a9900f5b3f2d5a7d10de3e124f7012ecd0b8b5 SHA512 2e67e5399c57a587e2afac1a412919faf383e4bfa00011ebf54bc3d4af6a353890500463b5f8a138fac7079eccec6b590c161be1419c5193d924fd1be1377f49
-EBUILD petsc-3.12.1.ebuild 5431 BLAKE2B 06e00d3f76c1eb2548fb2973014a7f674ecd2bb3b8928b12fa531acf3704fc8a85d22c194ad3d07c2ba470e228ccb4c5393b9f819e1a914d82dec6da2dd29e5b SHA512 2bfe62beb35946bf365925bc4b7b5c790f45fe6a3a37e45de420b69b983eba7d0d723a0eee3fa5e712a8abf87974baaf6120e8414f99a80dc5b353f5f90654e1
+DIST petsc-3.13.0.tar.gz 35080264 BLAKE2B 0ac58e53751dbc6e053e3591cdf2363194e0cf7a493f252d879031e0135da16fa24e66974dd7bf07ce18558a75f8dd794e87f96590ad9e550d11edfeb462f727 SHA512 0590bb63d9c6dfd6ac03b1b88e5a8c11d42a0fd014084603d4d085060b126aa4341b4ec3a4d2b12146b971da327ccc7ede370e5633282bf44f269465aea32953
+DIST petsc-3.13.1.tar.gz 35097687 BLAKE2B fccf64fd3694deffdd0dc561069ffa7e9342fe279b5c9123edeb011df931874083839d27b7b9a0c63faea6487b104b54fd4ce68a88a074c82de91e8baaf270b0 SHA512 41c3138a6ae6c1f2d9077b464c6aeda96287e5a76849582b8f432e2ee93d2594a78ba2181eac0054a77b6165692be5f1a057049313f2be9743d4246383dfdc77
+EBUILD petsc-3.13.0.ebuild 5335 BLAKE2B 82629d09778a4fb2c2c2c975ac9a864d2cc1b3f134f072257861ea9e4309730df7ea9930fa418b156f13384627ac5cd61ac91a6fccbe97595a23ac76bff2301a SHA512 351b627578c0be08fef91ee42a15f83c6e160bd4ccc7ff19570cf0f367332c815469ecac501a3ad90d2eb663d707674ce56424ea9a296c6c88f016eb31c3111e
+EBUILD petsc-3.13.1.ebuild 5335 BLAKE2B 82629d09778a4fb2c2c2c975ac9a864d2cc1b3f134f072257861ea9e4309730df7ea9930fa418b156f13384627ac5cd61ac91a6fccbe97595a23ac76bff2301a SHA512 351b627578c0be08fef91ee42a15f83c6e160bd4ccc7ff19570cf0f367332c815469ecac501a3ad90d2eb663d707674ce56424ea9a296c6c88f016eb31c3111e
 MISC metadata.xml 1131 BLAKE2B db15101bb24374026158a0b45bab1b4b38ab6869bb13fc1df48eef96ca003cea0a8b9118033a3d53c735cefd5ca7563e074d458aee32e038a39e68a6a91b7364 SHA512 19cf1bcddd8bc1378bf85c47b090dd684474f29896c1877bfbeb53a24b1112ed4bb6e823cbc830ee40c886727c6c90d0852081488b1df63f8b4f071d3d453630
diff --git a/sci-mathematics/petsc/files/petsc-3.12.1-do_not_run_mpiexec.patch b/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch
index 9c3d5047b0a6..4c46658dec71 100644
--- a/sci-mathematics/petsc/files/petsc-3.12.1-do_not_run_mpiexec.patch
+++ b/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch
@@ -1,14 +1,14 @@
 diff --git a/config/BuildSystem/config/packages/MPI.py b/config/BuildSystem/config/packages/MPI.py
-index c85bb504..7720eba9 100644
+index 7e424e71..ee502bd2 100644
 --- a/config/BuildSystem/config/packages/MPI.py
 +++ b/config/BuildSystem/config/packages/MPI.py
-@@ -209,26 +209,11 @@ shared libraries and run with --known-mpi-shared-libraries=1')
+@@ -210,28 +210,11 @@ shared libraries and run with --known-mpi-shared-libraries=1')
            raise RuntimeError('Could not locate MPIEXEC - please specify --with-mpiexec option')
        # Support for spaces and () in executable names; also needs to handle optional arguments at the end
        # TODO: This support for spaces and () should be moved to core BuildSystem
 -      self.mpiexec = self.mpiexec.replace(' ', '\\ ').replace('(', '\\(').replace(')', '\\)').replace('\ -',' -')
 -      if (hasattr(self, 'ompi_major_version') and int(self.ompi_major_version) >= 3):
--        (out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -help all', checkCommand = noCheck, timeout = 10, log = self.log)
+-        (out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -help all', checkCommand = noCheck, timeout = 60, log = self.log, threads = 1)
 -        if out.find('--oversubscribe') >=0:
 -          self.mpiexec = self.mpiexec + ' --oversubscribe'
 +      self.mpiexec = self.mpiexec + ' --oversubscribe'
@@ -16,17 +16,19 @@ index c85bb504..7720eba9 100644
      # using mpiexec environmental variables make sure mpiexec matches the MPI libraries and save the variables for testing in PetscInitialize()
      # the variable HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE is not currently used. PetscInitialize() can check the existence of the environmental variable to
      # determine if the program has been started with the correct mpiexec (will only be set for parallel runs so not clear how to check appropriately)
--    (out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -n 1 printenv', checkCommand = noCheck, timeout = 10, log = self.log)
--    if ret: raise RuntimeError('Unable to run '+self.mpiexec+' with option "-n 1"\n'+err)
--    if out.find('MPIR_CVAR_CH3') > -1:
--      if hasattr(self,'ompi_major_version'): raise RuntimeError("Your libraries are from OpenMPI but it appears your mpiexec is from MPICH");
--      self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPIR_CVAR_CH3')
--    elif  out.find('MPIR_CVAR_CH3') > -1:
--      if hasattr(self,'ompi_major_version'): raise RuntimeError("Your libraries are from OpenMPI but it appears your mpiexec is from MPICH");
--      self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPICH')
--    elif out.find('OMPI_COMM_WORLD_SIZE') > -1:
--      if hasattr(self,'mpich_numversion'): raise RuntimeError("Your libraries are from MPICH but it appears your mpiexec is from OpenMPI");
--      self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'OMP')
+-    (out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -n 1 printenv', checkCommand = noCheck, timeout = 60, threads = 1, log = self.log)
+-    if ret:
+-      self.logWrite('Unable to run '+self.mpiexec+' with option "-n 1 printenv"\nThis could be ok, some MPI implementations such as SGI produce a non-zero status with non-MPI programs\n'+out+err)
+-    else:
+-      if out.find('MPIR_CVAR_CH3') > -1:
+-        if hasattr(self,'ompi_major_version'): raise RuntimeError("Your libraries are from OpenMPI but it appears your mpiexec is from MPICH");
+-        self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPIR_CVAR_CH3')
+-      elif  out.find('MPIR_CVAR_CH3') > -1:
+-        if hasattr(self,'ompi_major_version'): raise RuntimeError("Your libraries are from OpenMPI but it appears your mpiexec is from MPICH");
+-        self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPICH')
+-      elif out.find('OMPI_COMM_WORLD_SIZE') > -1:
+-        if hasattr(self,'mpich_numversion'): raise RuntimeError("Your libraries are from MPICH but it appears your mpiexec is from OpenMPI");
+-        self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'OMP')
+ 
      self.addMakeMacro('MPIEXEC', self.mpiexec)
      self.mpiexec = self.mpiexec + ' -n 1'
- 
diff --git a/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.13.0-fix_sandbox_violation.patch
index 97f8dfed4d71..c0dfd53a0112 100644
--- a/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch
+++ b/sci-mathematics/petsc/files/petsc-3.13.0-fix_sandbox_violation.patch
@@ -1,15 +1,16 @@
 diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py
-index 92f190d..047c85b 100644
+index 860faf0f..87898811 100755
 --- a/config/PETSc/options/installDir.py
 +++ b/config/PETSc/options/installDir.py
-@@ -41,12 +41,6 @@ class Configure(config.base.Configure):
+@@ -40,13 +40,6 @@ class Configure(config.base.Configure):
        self.dir = os.path.abspath(os.path.expanduser(self.framework.argDB['prefix']))
        self.petscDir = self.dir
        self.petscArch = ''
 -      try:
 -        os.makedirs(os.path.join(self.dir,'PETScTestDirectory'))
 -        os.rmdir(os.path.join(self.dir,'PETScTestDirectory'))
--      except:
+-      except Exception as e:
+-        self.logPrint('Error trying to to test write permissions on directory '+str(e))
 -        self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs'
 -        self.installSudo = 'sudo '
      else:
diff --git a/sci-mathematics/petsc/files/petsc-3.12.1-make_hypre_configure.patch b/sci-mathematics/petsc/files/petsc-3.13.0-make_hypre_configure.patch
index 9460d57e4617..1453fd519e81 100644
--- a/sci-mathematics/petsc/files/petsc-3.12.1-make_hypre_configure.patch
+++ b/sci-mathematics/petsc/files/petsc-3.13.0-make_hypre_configure.patch
@@ -1,18 +1,18 @@
 diff --git a/config/BuildSystem/config/packages/hypre.py b/config/BuildSystem/config/packages/hypre.py
-index 869a1661..76067c8d 100644
+index 4d915c31..1b05a1ee 100644
 --- a/config/BuildSystem/config/packages/hypre.py
 +++ b/config/BuildSystem/config/packages/hypre.py
 @@ -5,10 +5,6 @@ class Configure(config.package.GNUPackage):
    def __init__(self, framework):
      config.package.GNUPackage.__init__(self, framework)
-     self.version         = '2.18.1'
+     #self.version         = '2.18.2'
 -    self.minversion      = '2.14'
 -    self.versionname     = 'HYPRE_RELEASE_VERSION'
 -    self.versioninclude  = 'HYPRE_config.h'
 -    self.requiresversion = 1
-     self.gitcommit       = 'v'+self.version
+     #self.gitcommit       = 'v'+self.version
+     self.gitcommit       = '93baaa8c9' # v2.18.2+valgrind-fix
      self.download        = ['git://https://github.com/hypre-space/hypre','https://github.com/hypre-space/hypre/archive/'+self.gitcommit+'.tar.gz']
-     self.functions       = ['HYPRE_IJMatrixCreate']
 diff --git a/include/petsc/private/petschypre.h b/include/petsc/private/petschypre.h
 index 81ca7136..b403e70e 100644
 --- a/include/petsc/private/petschypre.h
@@ -31,7 +31,7 @@ index 81ca7136..b403e70e 100644
    With scalar type == real, HYPRE_Complex == PetscScalar;
    With scalar type == complex,  HYPRE_Complex is double __complex__ while PetscScalar may be std::complex<double>
 diff --git a/src/mat/impls/hypre/mhypre.c b/src/mat/impls/hypre/mhypre.c
-index 8e8fe678..3533b99a 100644
+index 0f7470e6..cce3e2b0 100644
 --- a/src/mat/impls/hypre/mhypre.c
 +++ b/src/mat/impls/hypre/mhypre.c
 @@ -15,10 +15,6 @@
@@ -42,10 +42,10 @@ index 8e8fe678..3533b99a 100644
 -#define  hypre_ParCSRMatrixClone(A,B) hypre_ParCSRMatrixCompleteClone(A)
 -#endif
 -
- PETSC_INTERN PetscErrorCode MatPtAP_IS_XAIJ(Mat,Mat,MatReuse,PetscReal,Mat*);
- 
  static PetscErrorCode MatHYPRE_CreateFromMat(Mat,Mat_HYPRE*);
-@@ -65,7 +61,6 @@ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat A_d, Mat A_o, HYPRE_IJMat
+ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat,Mat,HYPRE_IJMatrix);
+ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat,HYPRE_IJMatrix);
+@@ -63,7 +59,6 @@ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat A_d, Mat A_o, HYPRE_IJMat
          nnz_o[i] = 0;
        }
      }
@@ -53,7 +53,7 @@ index 8e8fe678..3533b99a 100644
      { /* If we don't do this, the columns of the matrix will be all zeros! */
        hypre_AuxParCSRMatrix *aux_matrix;
        aux_matrix = (hypre_AuxParCSRMatrix*)hypre_IJMatrixTranslator(ij);
-@@ -75,9 +70,6 @@ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat A_d, Mat A_o, HYPRE_IJMat
+@@ -73,9 +68,6 @@ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat A_d, Mat A_o, HYPRE_IJMat
        aux_matrix = (hypre_AuxParCSRMatrix*)hypre_IJMatrixTranslator(ij);
        hypre_AuxParCSRMatrixNeedAux(aux_matrix) = 1;
      }
@@ -63,7 +63,7 @@ index 8e8fe678..3533b99a 100644
      ierr = PetscFree(nnz_d);CHKERRQ(ierr);
      ierr = PetscFree(nnz_o);CHKERRQ(ierr);
    }
-@@ -235,11 +227,7 @@ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat A, HYPRE_IJMatrix ij)
+@@ -233,11 +225,7 @@ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat A, HYPRE_IJMatrix ij)
    /* need to shift the diag column indices (hdiag->j) back to global numbering since hypre is expecting this */
    hjj = hdiag->j;
    pjj = pdiag->j;
@@ -75,7 +75,7 @@ index 8e8fe678..3533b99a 100644
    ierr = PetscArraycpy(hdiag->data,pdiag->a,pdiag->nz);CHKERRQ(ierr);
    if (sameint) {
      ierr = PetscArraycpy(hoffd->i,poffd->i,pA->A->rmap->n + 1);CHKERRQ(ierr);
-@@ -249,12 +237,8 @@ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat A, HYPRE_IJMatrix ij)
+@@ -247,12 +235,8 @@ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat A, HYPRE_IJMatrix ij)
  
    /* need to move the offd column indices (hoffd->j) back to global numbering since hypre is expecting this
       If we hacked a hypre a bit more we might be able to avoid this step */
diff --git a/sci-mathematics/petsc/petsc-3.12.1.ebuild b/sci-mathematics/petsc/petsc-3.13.0.ebuild
index 845d7ff75d69..961ff927f725 100644
--- a/sci-mathematics/petsc/petsc-3.12.1.ebuild
+++ b/sci-mathematics/petsc/petsc-3.13.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6,7,8} )
 
 inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
 
@@ -54,17 +54,11 @@ DEPEND="${RDEPEND}
 
 PATCHES=(
 	"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch
-	"${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch
-	"${FILESDIR}"/${PN}-3.12.1-make_hypre_configure.patch
-	"${FILESDIR}"/${PN}-3.12.1-do_not_run_mpiexec.patch
+	"${FILESDIR}"/${PN}-3.13.0-fix_sandbox_violation.patch
+	"${FILESDIR}"/${PN}-3.13.0-make_hypre_configure.patch
+	"${FILESDIR}"/${PN}-3.13.0-do_not_run_mpiexec.patch
 )
 
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
 # petsc uses --with-blah=1 and --with-blah=0 to en/disable options
 petsc_enable() {
 	use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0"
diff --git a/sci-mathematics/petsc/petsc-3.11.3.ebuild b/sci-mathematics/petsc/petsc-3.13.1.ebuild
index 50ce3b7f6631..961ff927f725 100644
--- a/sci-mathematics/petsc/petsc-3.11.3.ebuild
+++ b/sci-mathematics/petsc/petsc-3.13.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6,7,8} )
 
 inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
 
@@ -36,7 +36,7 @@ RDEPEND="
 	boost? ( dev-libs/boost )
 	fftw? ( sci-libs/fftw:3.0[mpi?] )
 	hdf5? ( sci-libs/hdf5[mpi?] )
-	hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] )
+	hypre? ( >=sci-libs/hypre-2.18.0[mpi?] )
 	metis? ( >=sci-libs/parmetis-4 )
 	mpi? ( virtual/mpi[cxx?,fortran?] )
 	mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
@@ -53,16 +53,12 @@ DEPEND="${RDEPEND}
 "
 
 PATCHES=(
-	"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \
-	"${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch
+	"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch
+	"${FILESDIR}"/${PN}-3.13.0-fix_sandbox_violation.patch
+	"${FILESDIR}"/${PN}-3.13.0-make_hypre_configure.patch
+	"${FILESDIR}"/${PN}-3.13.0-do_not_run_mpiexec.patch
 )
 
-src_prepare() {
-	default
-
-	sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
 # petsc uses --with-blah=1 and --with-blah=0 to en/disable options
 petsc_enable() {
 	use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0"
@@ -157,23 +153,23 @@ src_configure() {
 		$(use_with hdf5) \
 		$(petsc_with hypre hypre \
 			/usr/include/hypre -lHYPRE) \
-		$(petsc_with sparse suitesparse) \
+		$(use_with sparse suitesparse) \
 		$(petsc_with superlu superlu \
 			/usr/include/superlu -lsuperlu) \
-		$(petsc_with X x) \
-		$(petsc_with X x11) \
+		$(use_with X x) \
+		$(use_with X x11) \
 		$(petsc_with scotch ptscotch \
 			/usr/include/scotch \
 		[-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \
 		$(petsc_with mumps scalapack \
 			/usr/include/scalapack -lscalapack) \
-		$(petsc_with mumps mumps \
+		$(use_with mumps mumps \
 			/usr/include \
 			[-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \
 		--with-imagemagick=0 \
 		--with-python=0 \
-		$(petsc_with boost) \
-		$(petsc_with fftw)
+		$(use_with boost) \
+		$(use_with fftw)
 }
 
 src_install() {