Possible Memory problem with foam extend 4.0

HenrikJohansson · March 8, 2018, 08:02

Hi

I been analyzing a turbine with MRF, mixing planes, cyclic GGi:s and a real gas fluid. It works well with a coarse mesh.
I have now switched to a more powerfull computer and tested my coarse mesh case. Everything works fine.

So I refined my mesh from 1M cells to 8M for better accuracy.
My mesh have good quality and when running checkMesh -allGeometry -allTopology in openFOAM it shows no error.

But when I do any command(checkMesh, decomposePar, steadyUniversalMRFFoam) in foam extend i get the following error.

From google I get the solution that it has something to do with memory swapping?
My computer have 55GB ram and six Intel i7-3930 Cores and I'm running Ubuntu 16.04.

Code:

/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | foam-extend: Open Source CFD                    |
|  \\    /   O peration     | Version:     4.0                                |
|   \\  /    A nd           | Web:         http://www.foam-extend.org         |
|    \\/     M anipulation  | For copyright notice see file Copyright         |
\*---------------------------------------------------------------------------*/
Build    : 4.0-54c9f83b540c
Exec     : checkMesh -allTopology -allGeometry
Date     : Mar 08 2018
Time     : 12:26:41
Host     : henrik-linux
PID      : 17652
CtrlDict : "/media/henrik/Scratchen/OpenFOAM/Turbine_3D_2018_03_08_4Stage/system/controlDict"
Case     : /media/henrik/Scratchen/OpenFOAM/Turbine_3D_2018_03_08_4Stage
nProcs   : 1
SigFpe   : Enabling floating point exception trapping (FOAM_SIGFPE).

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create polyMesh for time = 0

Initializing the GGI interpolator between master/shadow patches: StatorLeft1_CyclicGgi/StatorRight1_CyclicGgi
Initializing the GGI interpolator between master/shadow patches: RotorLeft1_CyclicGgi/RotorRight1_CyclicGgi
Initializing the GGI interpolator between master/shadow patches: StatorLeft2_CyclicGgi/StatorRight2_CyclicGgi
Initializing the GGI interpolator between master/shadow patches: RotorLeft2_CyclicGgi/RotorRight2_CyclicGgi
Initializing the GGI interpolator between master/shadow patches: StatorLeft3_CyclicGgi/StatorRight3_CyclicGgi
Initializing the GGI interpolator between master/shadow patches: RotorLeft3_CyclicGgi/RotorRight3_CyclicGgi
Initializing the GGI interpolator between master/shadow patches: StatorLeft4_CyclicGgi/StatorRight4_CyclicGgi
Initializing the GGI interpolator between master/shadow patches: RotorLeft4_CyclicGgi/RotorRight4_CyclicGgi
*** Error in `checkMesh': corrupted size vs. prev_size: 0x000000002671c5f0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f6f7601d7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x80dfb)[0x7f6f76026dfb]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f6f7602a53c]
/home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfoam.so(_ZNK4Foam16GGIInterpolationINS_14PrimitivePatchINS_4faceENS_4ListERKNS_5FieldINS_6VectorIdEEEES6_EESA_E19maskedSlaveToMasterIS6_EEvRKNS4_IT_EERSE_RKNS3_IiEE+0x23c)[0x7f6f7758c2ac]
/home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfoam.so(_ZNK4Foam12ggiPolyPatch11interpolateINS_6VectorIdEEEENS_3tmpINS_5FieldIT_EEEERKS7_+0x271)[0x7f6f7758e3f1]
/home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfoam.so(_ZNK4Foam12ggiPolyPatch24calcReconFaceCellCentresEv+0x179)[0x7f6f7757b7a9]
/home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfoam.so(_ZNK4Foam12ggiPolyPatch20reconFaceCellCentresEv+0x19)[0x7f6f7757ba39]
/home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfoam.so(_ZN4Foam16polyBoundaryMesh10updateMeshEv+0x2ae)[0x7f6f775bbebe]
/home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfoam.so(_ZN4Foam8polyMeshC1ERKNS_8IOobjectE+0xfff)[0x7f6f775f038f]
checkMesh[0x408155]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f6f75fc6830]
checkMesh[0x408969]
======= Memory map: ========
00400000-0041e000 r-xp 00000000 08:22 5116555                            /home/henrik/foam/foam-extend-4.0/applications/bin/linux64GccDPOpt/checkMesh
0061d000-0061e000 r--p 0001d000 08:22 5116555                            /home/henrik/foam/foam-extend-4.0/applications/bin/linux64GccDPOpt/checkMesh
0061e000-0061f000 rw-p 0001e000 08:22 5116555                            /home/henrik/foam/foam-extend-4.0/applications/bin/linux64GccDPOpt/checkMesh
01eaf000-26e20000 rw-p 00000000 00:00 0                                  [heap]
7f6f14000000-7f6f14021000 rw-p 00000000 00:00 0 
7f6f14021000-7f6f18000000 ---p 00000000 00:00 0 
7f6f1b09b000-7f6f53454000 rw-p 00000000 00:00 0 
7f6f5374c000-7f6f73a1e000 rw-p 00000000 00:00 0 
7f6f73a1e000-7f6f73a87000 r-xp 00000000 08:22 4986835                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/liblduSolvers.so
7f6f73a87000-7f6f73c86000 ---p 00069000 08:22 4986835                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/liblduSolvers.so
7f6f73c86000-7f6f73c88000 r--p 00068000 08:22 4986835                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/liblduSolvers.so
7f6f73c88000-7f6f73c89000 rw-p 0006a000 08:22 4986835                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/liblduSolvers.so
7f6f73c89000-7f6f73c8a000 rw-p 00000000 00:00 0 
7f6f73c8a000-7f6f73c95000 r-xp 00000000 08:22 6820588                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f6f73c95000-7f6f73e94000 ---p 0000b000 08:22 6820588                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f6f73e94000-7f6f73e95000 r--p 0000a000 08:22 6820588                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f6f73e95000-7f6f73e96000 rw-p 0000b000 08:22 6820588                    /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f6f73e96000-7f6f73e9c000 rw-p 00000000 00:00 0 
7f6f73e9c000-7f6f73ea7000 r-xp 00000000 08:22 6820768                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f6f73ea7000-7f6f740a6000 ---p 0000b000 08:22 6820768                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f6f740a6000-7f6f740a7000 r--p 0000a000 08:22 6820768                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f6f740a7000-7f6f740a8000 rw-p 0000b000 08:22 6820768                    /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f6f740a8000-7f6f740be000 r-xp 00000000 08:22 6815830                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7f6f740be000-7f6f742bd000 ---p 00016000 08:22 6815830                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7f6f742bd000-7f6f742be000 r--p 00015000 08:22 6815830                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7f6f742be000-7f6f742bf000 rw-p 00016000 08:22 6815830                    /lib/x86_64-linux-gnu/libnsl-2.23.so
7f6f742bf000-7f6f742c1000 rw-p 00000000 00:00 0 
7f6f742c1000-7f6f742c9000 r-xp 00000000 08:22 6820489                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f6f742c9000-7f6f744c8000 ---p 00008000 08:22 6820489                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f6f744c8000-7f6f744c9000 r--p 00007000 08:22 6820489                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f6f744c9000-7f6f744ca000 rw-p 00008000 08:22 6820489                    /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f6f744ca000-7f6f744d3000 r-xp 00000000 08:22 1844006                    /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.1
7f6f744d3000-7f6f746d2000 ---p 00009000 08:22 1844006                    /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.1
7f6f746d2000-7f6f746d3000 r--p 00008000 08:22 1844006                    /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.1
7f6f746d3000-7f6f746d4000 rw-p 00009000 08:22 1844006                    /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.1
7f6f746d4000-7f6f746de000 r-xp 00000000 08:22 1838556                    /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7f6f746de000-7f6f748dd000 ---p 0000a000 08:22 1838556                    /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7f6f748dd000-7f6f748de000 r--p 00009000 08:22 1838556                    /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7f6f748de000-7f6f748df000 rw-p 0000a000 08:22 1838556                    /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7f6f748df000-7f6f748e1000 r-xp 00000000 08:22 6820488                    /lib/x86_64-linux-gnu/libutil-2.23.so
7f6f748e1000-7f6f74ae0000 ---p 00002000 08:22 6820488                    /lib/x86_64-linux-gnu/libutil-2.23.so
7f6f74ae0000-7f6f74ae1000 r--p 00001000 08:22 6820488                    /lib/x86_64-linux-gnu/libutil-2.23.so
7f6f74ae1000-7f6f74ae2000 rw-p 00002000 08:22 6820488                    /lib/x86_64-linux-gnu/libutil-2.23.so
7f6f74ae2000-7f6f74b1b000 r-xp 00000000 08:22 1845085                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.6.8
7f6f74b1b000-7f6f74d1a000 ---p 00039000 08:22 1845085                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.6.8
7f6f74d1a000-7f6f74d1b000 r--p 00038000 08:22 1845085                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.6.8
7f6f74d1b000-7f6f74d1c000 rw-p 00039000 08:22 1845085                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.6.8
7f6f74d1c000-7f6f74dac000 r-xp 00000000 08:22 1976508                    /usr/lib/openmpi/lib/libopen-pal.so.13.0.2
7f6f74dac000-7f6f74fac000 ---p 00090000 08:22 1976508                    /usr/lib/openmpi/lib/libopen-pal.so.13.0.2
7f6f74fac000-7f6f74fb0000 r--p 00090000 08:22 1976508                    /usr/lib/openmpi/lib/libopen-pal.so.13.0.2
7f6f74fb0000-7f6f74fb4000 rw-p 00094000 08:22 1976508                    /usr/lib/openmpi/lib/libopen-pal.so.13.0.2
7f6f74fb4000-7f6f74fb9000 rw-p 00000000 00:00 0 
7f6f74fb9000-7f6f7502e000 r-xp 00000000 08:22 1976504                    /usr/lib/openmpi/lib/libopen-rte.so.12.0.2
7f6f7502e000-7f6f7522d000 ---p 00075000 08:22 1976504                    /usr/lib/openmpi/lib/libopen-rte.so.12.0.2
7f6f7522d000-7f6f7522e000 r--p 00074000 08:22 1976504                    /usr/lib/openmpi/lib/libopen-rte.so.12.0.2
7f6f7522e000-7f6f75231000 rw-p 00075000 08:22 1976504                    /usr/lib/openmpi/lib/libopen-rte.so.12.0.2
7f6f75231000-7f6f75233000 rw-p 00000000 00:00 0 
7f6f75233000-7f6f75240000 r-xp 00000000 08:22 1845092                    /usr/lib/libibverbs.so.1.0.0
7f6f75240000-7f6f75440000 ---p 0000d000 08:22 1845092                    /usr/lib/libibverbs.so.1.0.0
7f6f75440000-7f6f75441000 r--p 0000d000 08:22 1845092                    /usr/lib/libibverbs.so.1.0.0
7f6f75441000-7f6f75442000 rw-p 0000e000 08:22 1845092                    /usr/lib/libibverbs.so.1.0.0
7f6f75442000-7f6f7545a000 r-xp 00000000 08:22 6815835                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7f6f7545a000-7f6f75659000 ---p 00018000 08:22 6815835                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7f6f75659000-7f6f7565a000 r--p 00017000 08:22 6815835                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7f6f7565a000-7f6f7565b000 rw-p 00018000 08:22 6815835                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7f6f7565b000-7f6f7565f000 rw-p 00000000 00:00 0 
7f6f7565f000-7f6f75678000 r-xp 00000000 08:22 6820658                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7f6f75678000-7f6f75877000 ---p 00019000 08:22 6820658                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7f6f75877000-7f6f75878000 r--p 00018000 08:22 6820658                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7f6f75878000-7f6f75879000 rw-p 00019000 08:22 6820658                    /lib/x86_64-linux-gnu/libz.so.1.2.8
7f6f75879000-7f6f7592b000 r-xp 00000000 08:22 1976501                    /usr/lib/openmpi/lib/libmpi.so.12.0.2
7f6f7592b000-7f6f75b2b000 ---p 000b2000 08:22 1976501                    /usr/lib/openmpi/lib/libmpi.so.12.0.2
7f6f75b2b000-7f6f75b2c000 r--p 000b2000 08:22 1976501                    /usr/lib/openmpi/lib/libmpi.so.12.0.2
7f6f75b2c000-7f6f75b3c000 rw-p 000b3000 08:22 1976501                    /usr/lib/openmpi/lib/libmpi.so.12.0.2
7f6f75b3c000-7f6f75b4f000 rw-p 00000000 00:00 0 
7f6f75b4f000-7f6f75b72000 r-xp 00000000 08:22 4986706                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/liblagrangian.so
7f6f75b72000-7f6f75d72000 ---p 00023000 08:22 4986706                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/liblagrangian.so
7f6f75d72000-7f6f75d73000 r--p 00023000 08:22 4986706                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/liblagrangian.so
7f6f75d73000-7f6f75d74000 rw-p 00024000 08:22 4986706                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/liblagrangian.so
7f6f75d74000-7f6f75da4000 r-xp 00000000 08:22 4986693                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libdecompositionMethods.so
7f6f75da4000-7f6f75fa4000 ---p 00030000 08:22 4986693                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libdecompositionMethods.so
7f6f75fa4000-7f6f75fa5000 r--p 00030000 08:22 4986693                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libdecompositionMethods.so
7f6f75fa5000-7f6f75fa6000 rw-p 00031000 08:22 4986693                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libdecompositionMethods.so
7f6f75fa6000-7f6f76166000 r-xp 00000000 08:22 6815836                    /lib/x86_64-linux-gnu/libc-2.23.so
7f6f76166000-7f6f76366000 ---p 001c0000 08:22 6815836                    /lib/x86_64-linux-gnu/libc-2.23.so
7f6f76366000-7f6f7636a000 r--p 001c0000 08:22 6815836                    /lib/x86_64-linux-gnu/libc-2.23.so
7f6f7636a000-7f6f7636c000 rw-p 001c4000 08:22 6815836                    /lib/x86_64-linux-gnu/libc-2.23.so
7f6f7636c000-7f6f76370000 rw-p 00000000 00:00 0 
7f6f76370000-7f6f76386000 r-xp 00000000 08:22 6820505                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f6f76386000-7f6f76585000 ---p 00016000 08:22 6820505                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f6f76585000-7f6f76586000 rw-p 00015000 08:22 6820505                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f6f76586000-7f6f7668e000 r-xp 00000000 08:22 6815828                    /lib/x86_64-linux-gnu/libm-2.23.so
7f6f7668e000-7f6f7688d000 ---p 00108000 08:22 6815828                    /lib/x86_64-linux-gnu/libm-2.23.so
7f6f7688d000-7f6f7688e000 r--p 00107000 08:22 6815828                    /lib/x86_64-linux-gnu/libm-2.23.so
7f6f7688e000-7f6f7688f000 rw-p 00108000 08:22 6815828                    /lib/x86_64-linux-gnu/libm-2.23.so
7f6f7688f000-7f6f76a01000 r-xp 00000000 08:22 1835407                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f6f76a01000-7f6f76c01000 ---p 00172000 08:22 1835407                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f6f76c01000-7f6f76c0b000 r--p 00172000 08:22 1835407                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f6f76c0b000-7f6f76c0d000 rw-p 0017c000 08:22 1835407                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f6f76c0d000-7f6f76c11000 rw-p 00000000 00:00 0 
7f6f76c11000-7f6f76c18000 r-xp 00000000 08:22 6820769                    /lib/x86_64-linux-gnu/librt-2.23.so
7f6f76c18000-7f6f76e17000 ---p 00007000 08:22 6820769                    /lib/x86_64-linux-gnu/librt-2.23.so
7f6f76e17000-7f6f76e18000 r--p 00006000 08:22 6820769                    /lib/x86_64-linux-gnu/librt-2.23.so
7f6f76e18000-7f6f76e19000 rw-p 00007000 08:22 6820769                    /lib/x86_64-linux-gnu/librt-2.23.so
7f6f76e19000-7f6f76e1c000 r-xp 00000000 08:22 6815841                    /lib/x86_64-linux-gnu/libdl-2.23.so
7f6f76e1c000-7f6f7701b000 ---p 00003000 08:22 6815841                    /lib/x86_64-linux-gnu/libdl-2.23.so
7f6f7701b000-7f6f7701c000 r--p 00002000 08:22 6815841                    /lib/x86_64-linux-gnu/libdl-2.23.so
7f6f7701c000-7f6f7701d000 rw-p 00003000 08:22 6815841                    /lib/x86_64-linux-gnu/libdl-2.23.so
7f6f7701d000-7f6f77bdc000 r-xp 00000000 08:22 4987659                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfoam.so
7f6f77bdc000-7f6f77ddb000 ---p 00bbf000 08:22 4987659                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfoam.so
7f6f77ddb000-7f6f77e05000 r--p 00bbe000 08:22 4987659                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfoam.so
7f6f77e05000-7f6f77e12000 rw-p 00be8000 08:22 4987659                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libfoam.so
7f6f77e12000-7f6f77e31000 rw-p 00000000 00:00 0 
7f6f77e31000-7f6f78087000 r-xp 00000000 08:22 4986709                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libmeshTools.so
7f6f78087000-7f6f78286000 ---p 00256000 08:22 4986709                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libmeshTools.so
7f6f78286000-7f6f7828c000 r--p 00255000 08:22 4986709                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libmeshTools.so
7f6f7828c000-7f6f78290000 rw-p 0025b000 08:22 4986709                    /home/henrik/foam/foam-extend-4.0/lib/linux64GccDPOpt/libmeshTools.so
7f6f78290000-7f6f78293000 rw-p 00000000 00:00 0 
7f6f78293000-7f6f782b9000 r-xp 00000000 08:22 6815833                    /lib/x86_64-linux-gnu/ld-2.23.so
7f6f782f2000-7f6f78394000 rw-p 00000000 00:00 0 
7f6f783d5000-7f6f7848a000 rw-p 00000000 00:00 0 
7f6f78493000-7f6f784b8000 rw-p 00000000 00:00 0 
7f6f784b8000-7f6f784b9000 r--p 00025000 08:22 6815833                    /lib/x86_64-linux-gnu/ld-2.23.so
7f6f784b9000-7f6f784ba000 rw-p 00026000 08:22 6815833                    /lib/x86_64-linux-gnu/ld-2.23.so
7f6f784ba000-7f6f784bb000 rw-p 00000000 00:00 0 
7fff3563c000-7fff3565f000 rw-p 00000000 00:00 0                          [stack]
7fff356ef000-7fff356f2000 r--p 00000000 00:00 0                          [vvar]
7fff356f2000-7fff356f4000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
./RunParallel: line 74: 17652 Aborted                 (core dumped) checkMesh -allTopology -allGeometry

HenrikJohansson · April 19, 2018, 09:07

Solved:

Turns out the cyclicGGI does not like when the mesh is not similar on both faces. Made my mesh more structured and similar on the faces and the error went away

April 19, 2018, 09:07		#2
HenrikJohansson Member Henrik Johansson Join Date: Oct 2017 Location: Gothenburg Posts: 38 Rep Power: 9	Solved: Turns out the cyclicGGI does not like when the mesh is not similar on both faces. Made my mesh more structured and similar on the faces and the error went away __________________ / Henrik Johansson

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