# FreeFem++ PETSc configuration problem in Linux **URL:** \ **Category:** FreeFEM installation\ **Created:** [August 21, 2020, 10:17am UTC](https://community.freefem.org/t/freefem-petsc-configuration-problem-in-linux/542 "2020-08-21T10:17:44Z")\ **Posts on this page:** 1\ **Showing post:** 13
**Author:** ![vaalea](https://avatars.discourse-cdn.com/v4/letter/v/aca169/32.png) [@vaalea](https://community.freefem.org/u/vaalea)\ **Post date:** [August 25, 2020, 7:31am UTC](https://community.freefem.org/t/freefem-petsc-configuration-problem-in-linux/542/13 "2020-08-25T07:31:18Z")
## Dear Prj, Sorry for late reply. I did what you told me and here is the output. # make -j4 check make check-TESTS make[1]: Entering directory `/home/yim/FreeFem-sources/examples/hpddm' make[2]: Entering directory `/home/yim/FreeFem-sources/examples/hpddm’ XFAIL: withPartitioning.edp XFAIL: buildRecursive.edp XFAIL: createPartition.edp XFAIL: reconstructDmesh.edp XFAIL: diffusion-2d.edp XFAIL: diffusion-mg-2d.edp XFAIL: diffusion-substructuring-2d.edp XFAIL: diffusion-substructuring-withPartitioning-2d.edp XFAIL: diffusion-3d.edp XFAIL: diffusion-simple-3d.edp XFAIL: diffusion-periodic-2d.edp XFAIL: elasticity-2d.edp XFAIL: elasticity-substructuring-2d.edp XFAIL: elasticity-3d.edp XFAIL: elasticity-simple-3d.edp PASS: elasticity-block.edp XFAIL: heat-2d.edp XFAIL: heat-io-2d.edp XFAIL: heat-3d.edp XFAIL: helmholtz-2d.edp XFAIL: helmholtz-mg-2d.edp XFAIL: iterative.edp XFAIL: maxwell-3d.edp XFAIL: stokes-2d.edp XFAIL: stokes-3d.edp XFAIL: stokes-io-3d.edp XFAIL: heat-torus-3d-surf.edp XFAIL: bratu-2d-PETSc.edp XFAIL: diffusion-2d-PETSc.edp XFAIL: diffusion-3d-PETSc.edp XFAIL: diffusion-periodic-2d-PETSc.edp XFAIL: diffusion-periodic-balanced-2d-PETSc.edp XFAIL: elasticity-2d-PETSc.edp XFAIL: elasticity-3d-PETSc.edp XFAIL: elasticity-SNES-3d-PETSc.edp XFAIL: heat-2d-PETSc.edp XFAIL: laplace-lagrange-PETSc.edp XFAIL: natural-convection-fieldsplit-2d-PETSc.edp XFAIL: neo-Hookean-2d-PETSc.edp XFAIL: newton-2d-PETSc.edp XFAIL: newton-adaptmesh-2d-PETSc.edp XFAIL: newton-vi-2d-PETSc.edp XFAIL: newton-vi-adaptmesh-2d-PETSc.edp XFAIL: block-PETSc.edp XFAIL: laplace-RT-2d-PETSc.edp XFAIL: stokes-2d-PETSc.edp XFAIL: stokes-fieldsplit-2d-PETSc.edp XFAIL: stokes-block-2d-PETSc.edp XFAIL: stokes-3d-PETSc.edp XFAIL: stokes-fieldsplit-3d-PETSc.edp XFAIL: transpose-solve-PETSc.edp XFAIL: bratu-hpddm-2d-PETSc.edp XFAIL: vi-2d-PETSc.edp PASS: orego-Tao-PETSc.edp XFAIL: heat-TS-2d-PETSc.edp XFAIL: heat-TS-RHS-2d-PETSc.edp XFAIL: advection-TS-2d-PETSc.edp PASS: toy-Tao-PETSc.edp XFAIL: minimal-surface-Tao-2d-PETSc.edp XFAIL: Schur-complement-PETSc.edp XFAIL: maxwell-2d-PETSc.edp XFAIL: maxwell-3d-PETSc.edp XFAIL: laplace-adapt-3d-PETSc.edp XFAIL: diffusion-mg-3d-PETSc.edp XFAIL: save-load-Dmesh.edp XFAIL: navier-stokes-2d-PETSc.edp XFAIL: transfer.edp SKIP: distributed-parmmg.edp SKIP: laplace-adapt-dist-3d-PETSc.edp XFAIL: laplace-2d-SLEPc.edp XFAIL: laplace-spherical-harmonics-2d-SLEPc.edp XFAIL: laplace-torus-2d-SLEPc.edp XFAIL: schrodinger-harmonic-oscillator-1d-SLEPc.edp XFAIL: schrodinger-square-well-1d-SLEPc.edp XFAIL: schrodinger-axial-well-2d-SLEPc.edp XFAIL: schrodinger-harmonic-oscillator-2d-SLEPc.edp XFAIL: laplace-beltrami-3d-surf-SLEPc.edp XFAIL: laplace-beltrami-3d-line-SLEPc.edp XFAIL: diffusion-2d-PETSc-complex.edp XFAIL: helmholtz-2d-PETSc-complex.edp XFAIL: helmholtz-mg-2d-PETSc-complex.edp XFAIL: maxwell-mg-3d-PETSc-complex.edp XFAIL: laplace-2d-SLEPc-complex.edp XFAIL: navier-stokes-2d-SLEPc-complex.edp XFAIL: helmholtz-3d-surf-PETSc-complex.edp XFAIL: helmholtz-3d-line-PETSc-complex.edp XFAIL: helmholtz-coupled-2d-PETSc-complex.edp # Testsuite summary for FreeFEM 4.6 # TOTAL: 87 # PASS: 3 # SKIP: 2 # XFAIL: 82 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[2]: Leaving directory `/home/yim/FreeFem-sources/examples/hpddm' make[1]: Leaving directory `/home/yim/FreeFem-sources/examples/hpddm’ * * * Most of them are XFAIL… What this means? When I see for example, diffusion-3d.edp.log, it says this. * * * ‘mpiexec’ -np 4 …/…/src/mpi/FreeFem+±mpi -nw ./diffusion-3d.edp Fatal error in PMPI\_Init\_thread: Other MPI error, error stack: MPIR\_Init\_thread(805)…: fail failed MPID\_Init(1859)…: channel initialization failed MPIDI\_CH3\_Init(126)…: fail failed MPID\_nem\_init\_ckpt(857)…: fail failed MPIDI\_CH3I\_Seg\_commit(427): PMI\_KVS\_Get returned 4 In: PMI\_Abort(69777679, Fatal error in PMPI\_Init\_thread: Other MPI error, error stack: MPIR\_Init\_thread(805)…: fail failed MPID\_Init(1859)…: channel initialization failed MPIDI\_CH3\_Init(126)…: fail failed MPID\_nem\_init\_ckpt(857)…: fail failed MPIDI\_CH3I\_Seg\_commit(427): PMI\_KVS\_Get returned 4) INTERNAL ERROR: invalid error code ffffffff (Ring Index out of range) in MPID\_nem\_gen2\_module\_get\_from\_bc:262 INTERNAL ERROR: invalid error code ffffffff (Ring Index out of range) in MPID\_nem\_gen2\_module\_get\_from\_bc:262 INTERNAL ERROR: invalid error code ffffffff (Ring Index out of range) in MPID\_nem\_gen2\_module\_get\_from\_bc:262 INTERNAL ERROR: invalid error code ffffffff (Ring Index out of range) in MPID\_nem\_gen2\_module\_get\_from\_bc:262 [1] Abort: Error code in polled desc! at line 2502 in file …/…/src/mpid/ch3/channels/nemesis/netmod/ofa/ofa\_init.c [2] Abort: Error code in polled desc! at line 2502 in file …/…/src/mpid/ch3/channels/nemesis/netmod/ofa/ofa\_init.c # =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 4159 RUNNING AT fidis = EXIT CODE: 9 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES # =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 4162 RUNNING AT fidis = EXIT CODE: 9 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES # Intel® MPI Library troubleshooting guide: [https://software.intel.com/node/561764](https://software.intel.com/node/561764) * * * ## HOWEVER, when I run the code with srun with slurm, I have good results. Do you want me to do the test agian with srun? — 0/4 - diffusion-3d.edp - input parameters: refinement factor = 1 - overlap = 1 – Cube nv=8 nt=6 nbe=12 kind= 6 – Cube nv=8 nt=6 nbe=12 kind= 6 – Cube nv=8 nt=6 nbe=12 kind= 6 – FESpace: Nb of Nodes 8 Nb of DoF 8 – FESpace: Nb of Nodes 8 Nb of DoF 8 – Cube nv=1331 nt=6000 nbe=1200 kind= 6 – Cube nv=1331 nt=6000 nbe=1200 kind= 6 – Build Nodes/DF on mesh : n.v. 1331, n. elmt. 6000, n b. elmt. 1200 – Build Nodes/DF on mesh : n.v. 1331, n. elmt. 6000, n b. elmt. 1200 nb of Nodes 6000 nb of DoF 6000 DFon=0001 nb of Nodes 6000 nb of DoF 6000 DFon=0001 – FESpace: Nb of Nodes 6000 Nb of DoF 6000 – FESpace: Nb of Nodes 1331 Nb of DoF 1331 – FESpace: Nb of Nodes 6000 Nb of DoF 6000 – FESpace: Nb of Nodes 1331 Nb of DoF 1331 — global mesh of 6000 elements (prior to refinement) partitioned with metis --metisESCOA: 4-way Edge-Cut: 4, Balance: 1.02 Nodal=0/Dual 1 (in 1.995611e-02) – FESpace: Nb of Nodes 400 Nb of DoF 400 – FESpace: Nb of Nodes 409 Nb of DoF 409 – FESpace: Nb of Nodes 662 Nb of DoF 662 – FESpace: Nb of Nodes 716 Nb of DoF 716 – Cube nv=8 nt=6 nbe=12 kind= 6 – FESpace: Nb of Nodes 8 Nb of DoF 8 – FESpace: Nb of Nodes 8 Nb of DoF 8 – Cube nv=1331 nt=6000 nbe=1200 kind= 6 – Cube nv=1331 nt=6000 nbe=1200 kind= 6 – Build Nodes/DF on mesh : n.v. 1331, n. elmt. 6000, n b. elmt. 1200 – Build Nodes/DF on mesh : n.v. 1331, n. elmt. 6000, n b. elmt. 1200 nb of Nodes 6000 nb of DoF 6000 DFon=0001 – FESpace: Nb of Nodes 6000 Nb of DoF 6000 nb of Nodes 6000 nb of DoF 6000 DFon=0001 – FESpace: Nb of Nodes 6000 Nb of DoF 6000 – FESpace: Nb of Nodes 1331 Nb of DoF 1331 – FESpace: Nb of Nodes 1331 Nb of DoF 1331 – FESpace: Nb of Nodes 392 Nb of DoF 392 – FESpace: Nb of Nodes 408 Nb of DoF 408 – FESpace: Nb of Nodes 645 Nb of DoF 645 – FESpace: Nb of Nodes 746 Nb of DoF 746 – Build Nodes/DF on mesh : n.v. 645, n. elmt. 2675, n b. elmt. 702 nb of Nodes 2675 nb of DoF 2675 DFon=0001 – FESpace: Nb of Nodes 2675 Nb of DoF 2675 – Build Nodes/DF on mesh : n.v. 716, n. elmt. 3013, n b. elmt. 752 – Build Nodes/DF on mesh : n.v. 662, n. elmt. 2756, n b. elmt. 714 nb of Nodes 3013 nb of DoF 3013 DFon=0001 – FESpace: Nb of Nodes 3013 Nb of DoF 3013 nb of Nodes 2756 nb of DoF 2756 DFon=0001 – FESpace: Nb of Nodes 2756 Nb of DoF 2756 – Build Nodes/DF on mesh : n.v. 746, n. elmt. 3174, n b. elmt. 764 nb of Nodes 3174 nb of DoF 3174 DFon=0001 – FESpace: Nb of Nodes 3174 Nb of DoF 3174 – FESpace: Nb of Nodes 513 Nb of DoF 513 – FESpace: Nb of Nodes 530 Nb of DoF 530 – FESpace: Nb of Nodes 547 Nb of DoF 547 – FESpace: Nb of Nodes 569 Nb of DoF 569 – FESpace: Nb of Nodes 513 Nb of DoF 513 – FESpace: Nb of Nodes 197 Nb of DoF 197 – FESpace: Nb of Nodes 530 Nb of DoF 530 – FESpace: Nb of Nodes 206 Nb of DoF 206 – FESpace: Nb of Nodes 513 Nb of DoF 513 – FESpace: Nb of Nodes 220 Nb of DoF 220 – FESpace: Nb of Nodes 513 Nb of DoF 513 – FESpace: Nb of Nodes 530 Nb of DoF 530 – FESpace: Nb of Nodes 220 Nb of DoF 220 – FESpace: Nb of Nodes 530 Nb of DoF 530 – FESpace: Nb of Nodes 547 Nb of DoF 547 – FESpace: Nb of Nodes 206 Nb of DoF 206 – FESpace: Nb of Nodes 547 Nb of DoF 547 – FESpace: Nb of Nodes 163 Nb of DoF 163 – FESpace: Nb of Nodes 547 Nb of DoF 547 – FESpace: Nb of Nodes 197 Nb of DoF 197 – FESpace: Nb of Nodes 547 Nb of DoF 547 – FESpace: Nb of Nodes 569 Nb of DoF 569 – FESpace: Nb of Nodes 163 Nb of DoF 163 – FESpace: Nb of Nodes 569 Nb of DoF 569 – FESpace: Nb of Nodes 220 Nb of DoF 220 – FESpace: Nb of Nodes 569 Nb of DoF 569 – FESpace: Nb of Nodes 220 Nb of DoF 220 – FESpace: Nb of Nodes 569 Nb of DoF 569 — partition of unity built (in 5.068111e-02) – FESpace: Nb of Nodes 645 Nb of DoF 645 – FESpace: Nb of Nodes 662 Nb of DoF 662 – FESpace: Nb of Nodes 716 Nb of DoF 716 – FESpace: Nb of Nodes 746 Nb of DoF 746 – FESpace: Nb of Nodes 513 Nb of DoF 513 – FESpace: Nb of Nodes 530 Nb of DoF 530 – Cube nv=8 nt=6 nbe=12 kind= 6 – FESpace: Nb of Nodes 547 Nb of DoF 547 – Cube nv=8 nt=6 nbe=12 kind= 6 – FESpace: Nb of Nodes 569 Nb of DoF 569 – Cube nv=8 nt=6 nbe=12 kind= 6 – Cube nv=8 nt=6 nbe=12 kind= 6 times: compile 0.06s, execution 0.29s, mpirank:1 times: compile 0.05s, execution 0.29s, mpirank:2 ######## We forget of deleting 0 Nb pointer, 0Bytes , mpirank 1, memory leak =956464 CodeAlloc : nb ptr 6807, size :631600 mpirank: 1 times: compile 0.05s, execution 0.29s, mpirank:3 ######## We forget of deleting 0 Nb pointer, 0Bytes , mpirank 2, memory leak =809072 CodeAlloc : nb ptr 6807, size :631600 mpirank: 2 ######## We forget of deleting 0 Nb pointer, 0Bytes , mpirank 3, memory leak =956480 CodeAlloc : nb ptr 6807, size :631600 mpirank: 3 times: compile 1.600000e-01s, execution 1.800000e-01s, mpirank:0 ######## We forget of deleting 0 Nb pointer, 0Bytes , mpirank 0, memory leak =809072 CodeAlloc : nb ptr 6807, size :631600 mpirank: 0 Ok: Normal End * * * --- _[View the full topic](https://community.freefem.org/t/freefem-petsc-configuration-problem-in-linux/542)._