Here is something about the libgomp.so
[root@localhost lib]# ldd --verbose libgomp.so
linux-vdso.so.1 => (0x00007ffcb13a0000)
librt.so.1 => /lib64/librt.so.1 (0x00007f6b261cb000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f6b25fad000)
libc.so.6 => /lib64/libc.so.6 (0x00007f6b25c19000)
/lib64/ld-linux-x86-64.so.2 (0x00007f6b265e7000)
Version information:
./libgomp.so:
librt.so.1 (GLIBC_2.2.5) => /lib64/librt.so.1
libpthread.so.0 (GLIBC_2.3.4) => /lib64/libpthread.so.0
libpthread.so.0 (GLIBC_2.2.5) => /lib64/libpthread.so.0
libc.so.6 (GLIBC_2.3) => /lib64/libc.so.6
libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
/lib64/librt.so.1:
libpthread.so.0 (GLIBC_2.2.5) => /lib64/libpthread.so.0
libpthread.so.0 (GLIBC_PRIVATE) => /lib64/libpthread.so.0
libc.so.6 (GLIBC_2.3.2) => /lib64/libc.so.6
libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
libc.so.6 (GLIBC_PRIVATE) => /lib64/libc.so.6
/lib64/libpthread.so.0:
ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-
64.so.2
ld-linux-x86-64.so.2 (GLIBC_2.2.5) => /lib64/ld-linux-x86-
64.so.2
ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-
64.so.2
libc.so.6 (GLIBC_2.3.2) => /lib64/libc.so.6
libc.so.6 (GLIBC_PRIVATE) => /lib64/libc.so.6
libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
/lib64/libc.so.6:
ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-
64.so.2
ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-
64.so.2
On Thursday, January 12, 2017 at 8:40:38 AM UTC+8, CatDog wrote:
>
> Hello, everyone
>
> I am testing the installation of pyfr1.5.0 on a single-core VPS on
> bandwagonhost with centos 6. Because the softwares' versions of the OS are
> very old, the python 3 is installed using anaconda, and the gcc 4.9.2 is
> installed using devtoolset-3 of RHSCL. All dependency and version number is
> satisified. But the test case gives me an error:
>
> [root@localhost euler_vortex_2d]# pyfr run -b openmp
> euler_vortex_2d.pyfrm euler_vortex_2d.ini
>
> *error msg:*
>
> Traceback (most recent call last):
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/util.py",
>
> line 32, in __call__
> KeyError: (<function OpenMPKernelProvider._build_kernel at
> 0x7f165ac5fb70>,
> b'\x80\x03X\x05\x00\x00\x00tfluxq\x00X^\x1e\x00\x00\n\n#include
> <omp.h>\n#include <stdlib.h>\n#include <tgmath.h>\n\n#define
> PYFR_ALIGN_BYTES 64\n#define SOA_SZ 8\n\n#define min(a, b) ((a) < (b) ? (a)
> : (b))\n#define max(a, b) ((a) > (b) ? (a) : (b))\n\n// Typedefs\ntypedef
> double fpdtype_t;\n\n// OpenMP static loop scheduling functions\n\nstatic
> inline int\ngcd(int a, int b)\n{\n return (a == 0) ? b : gcd(b % a,
> a);\n}\n\nstatic inline void\nloop_sched_1d(int n, int align, int *b, int
> *e)\n{\n int tid = omp_get_thread_num();\n int nth =
> omp_get_num_threads();\n\n // Round up n to be a multiple of nth\n
> int rn = n + nth - 1 - (n - 1) % nth;\n\n // Nominal tile size\n int
> sz = rn / nth;\n\n // Handle alignment\n sz += align - 1 - (sz - 1) %
> align;\n\n // Assign the starting and ending index\n *b = sz * tid;\n
> *e = min(*b + sz, n);\n\n // Clamp\n if (*b >= n)\n *b = *e
> = 0;\n}\n\nstatic inline void\nloop_sched_2d(int nrow, int ncol, int
> colalign,\n int *rowb, int *rowe, int *colb, int *cole)\n{\n
> int tid = omp_get_thread_num();\n int nth = omp_get_num_threads();\n\n
> // Distribute threads\n int nrowth = gcd(nrow, nth);\n int ncolth
> = nth / nrowth;\n\n // Row and column indices for our thread\n int
> rowix = tid / ncolth;\n int colix = tid % ncolth;\n\n // Round up
> ncol to be a multiple of ncolth\n int rncol = ncol + ncolth - 1 - (ncol
> - 1) % ncolth;\n\n // Nominal tile size\n int ntilerow = nrow /
> nrowth;\n int ntilecol = rncol / ncolth;\n\n // Handle column
> alignment\n ntilecol += colalign - 1 - (ntilecol - 1) % colalign;\n\n
> // Assign the starting and ending row to each thread\n *rowb = ntilerow
> * rowix;\n *rowe = *rowb + ntilerow;\n\n // Assign the starting and
> ending column to each thread\n *colb = ntilecol * colix;\n *cole =
> min(*colb + ntilecol, ncol);\n\n // Clamp\n if (*colb >= ncol)\n
> *colb = *cole = 0;\n}\n\n\n\n\n\n\n\n\n\nvoid tflux(int _ny, int _nx,
> fpdtype_t* __restrict__ f_v, int ldf, const fpdtype_t* __restrict__
> smats_v, int ldsmats, const fpdtype_t* __restrict__ u_v, int ldu)\n
> {\n #define X_IDX (_xi + _xj)\n
> #define X_IDX_AOSOA(v, nv) ((_xi/SOA_SZ*(nv) +
> (v))*SOA_SZ + _xj)\n int align = PYFR_ALIGN_BYTES /
> sizeof(fpdtype_t);\n #pragma omp parallel\n
> {\n \n int rb, re, cb, ce;\n
> loop_sched_2d(_ny, _nx, align, &rb, &re, &cb, &ce);\n
> int nci = ((ce - cb) / SOA_SZ)*SOA_SZ;\n
> for (int _y = rb; _y < re; _y++)\n {\n
> for (int _xi = cb; _xi < cb + nci; _xi += SOA_SZ)\n
> {\n #pragma omp simd\n
> for (int _xj = 0; _xj < SOA_SZ; _xj++)\n
> {\n \n // Compute the flux\n
> fpdtype_t ftemp[2][4];\n fpdtype_t p, v[2];\n {\n\n fpdtype_t
> invrho_ = 1.0/u_v[ldu*_y + X_IDX_AOSOA(0, 4)], E_ = u_v[ldu*_y +
> X_IDX_AOSOA(3, 4)];\n\n // Compute the velocities\n fpdtype_t
> rhov_[2];\n rhov_[0] = u_v[ldu*_y + X_IDX_AOSOA(1, 4)];\n v[0] =
> invrho_*rhov_[0];\n rhov_[1] = u_v[ldu*_y + X_IDX_AOSOA(2, 4)];\n
> v[1] = invrho_*rhov_[1];\n\n // Compute the pressure\n p =
> 0.3999999999999999*(E_ - 0.5*invrho_*((rhov_[0])*(rhov_[0]) +
> (rhov_[1])*(rhov_[1])));\n\n // Density and energy fluxes\n
> ftemp[0][0] = rhov_[0];\n ftemp[0][3] = (E_ + p)*v[0];\n ftemp[1][0]
> = rhov_[1];\n ftemp[1][3] = (E_ + p)*v[1];\n\n // Momentum fluxes\n
> ftemp[0][1] = rhov_[0]*v[0] + p;\n ftemp[0][2] = rhov_[0]*v[1];\n
> ftemp[1][1] = rhov_[1]*v[0];\n ftemp[1][2] = rhov_[1]*v[1] +
> p;\n\n};\n\n // Transform the fluxes\n f_v[(0*_ny + _y)*ldf +
> X_IDX_AOSOA(0, 4)] = smats_v[(0*_ny + _y)*ldsmats + X_IDX_AOSOA(0,
> 2)]*ftemp[0][0] + smats_v[(0*_ny + _y)*ldsmats + X_IDX_AOSOA(1,
> 2)]*ftemp[1][0];\n f_v[(0*_ny + _y)*ldf + X_IDX_AOSOA(1, 4)] =
> smats_v[(0*_ny + _y)*ldsmats + X_IDX_AOSOA(0, 2)]*ftemp[0][1] +
> smats_v[(0*_ny + _y)*ldsmats + X_IDX_AOSOA(1, 2)]*ftemp[1][1];\n
> f_v[(0*_ny + _y)*ldf + X_IDX_AOSOA(2, 4)] = smats_v[(0*_ny + _y)*ldsmats +
> X_IDX_AOSOA(0, 2)]*ftemp[0][2] + smats_v[(0*_ny + _y)*ldsmats +
> X_IDX_AOSOA(1, 2)]*ftemp[1][2];\n f_v[(0*_ny + _y)*ldf + X_IDX_AOSOA(3,
> 4)] = smats_v[(0*_ny + _y)*ldsmats + X_IDX_AOSOA(0, 2)]*ftemp[0][3] +
> smats_v[(0*_ny + _y)*ldsmats + X_IDX_AOSOA(1, 2)]*ftemp[1][3];\n
> f_v[(1*_ny + _y)*ldf + X_IDX_AOSOA(0, 4)] = smats_v[(1*_ny + _y)*ldsmats +
> X_IDX_AOSOA(0, 2)]*ftemp[0][0] + smats_v[(1*_ny + _y)*ldsmats +
> X_IDX_AOSOA(1, 2)]*ftemp[1][0];\n f_v[(1*_ny + _y)*ldf + X_IDX_AOSOA(1,
> 4)] = smats_v[(1*_ny + _y)*ldsmats + X_IDX_AOSOA(0, 2)]*ftemp[0][1] +
> smats_v[(1*_ny + _y)*ldsmats + X_IDX_AOSOA(1, 2)]*ftemp[1][1];\n
> f_v[(1*_ny + _y)*ldf + X_IDX_AOSOA(2, 4)] = smats_v[(1*_ny + _y)*ldsmats +
> X_IDX_AOSOA(0, 2)]*ftemp[0][2] + smats_v[(1*_ny + _y)*ldsmats +
> X_IDX_AOSOA(1, 2)]*ftemp[1][2];\n f_v[(1*_ny + _y)*ldf + X_IDX_AOSOA(3,
> 4)] = smats_v[(1*_ny + _y)*ldsmats + X_IDX_AOSOA(0, 2)]*ftemp[0][3] +
> smats_v[(1*_ny + _y)*ldsmats + X_IDX_AOSOA(1, 2)]*ftemp[1][3];\n\n
> }\n }\n
> for (int _xi = cb + nci, _xj = 0; _xj < ce - _xi;\n
> _xj++)\n {\n \n
> // Compute the flux\n fpdtype_t ftemp[2][4];\n fpdtype_t p, v[2];\n
> {\n\n fpdtype_t invrho_ = 1.0/u_v[ldu*_y + X_IDX_AOSOA(0, 4)], E_ =
> u_v[ldu*_y + X_IDX_AOSOA(3, 4)];\n\n // Compute the velocities\n
> fpdtype_t rhov_[2];\n rhov_[0] = u_v[ldu*_y + X_IDX_AOSOA(1, 4)];\n
> v[0] = invrho_*rhov_[0];\n rhov_[1] = u_v[ldu*_y + X_IDX_AOSOA(2,
> 4)];\n v[1] = invrho_*rhov_[1];\n\n // Compute the pressure\n p =
> 0.3999999999999999*(E_ - 0.5*invrho_*((rhov_[0])*(rhov_[0]) +
> (rhov_[1])*(rhov_[1])));\n\n // Density and energy fluxes\n
> ftemp[0][0] = rhov_[0];\n ftemp[0][3] = (E_ + p)*v[0];\n ftemp[1][0]
> = rhov_[1];\n ftemp[1][3] = (E_ + p)*v[1];\n\n // Momentum fluxes\n
> ftemp[0][1] = rhov_[0]*v[0] + p;\n ftemp[0][2] = rhov_[0]*v[1];\n
> ftemp[1][1] = rhov_[1]*v[0];\n ftemp[1][2] = rhov_[1]*v[1] +
> p;\n\n};\n\n // Transform the fluxes\n f_v[(0*_ny + _y)*ldf +
> X_IDX_AOSOA(0, 4)] = smats_v[(0*_ny + _y)*ldsmats + X_IDX_AOSOA(0,
> 2)]*ftemp[0][0] + smats_v[(0*_ny + _y)*ldsmats + X_IDX_AOSOA(1,
> 2)]*ftemp[1][0];\n f_v[(0*_ny + _y)*ldf + X_IDX_AOSOA(1, 4)] =
> smats_v[(0*_ny + _y)*ldsmats + X_IDX_AOSOA(0, 2)]*ftemp[0][1] +
> smats_v[(0*_ny + _y)*ldsmats + X_IDX_AOSOA(1, 2)]*ftemp[1][1];\n
> f_v[(0*_ny + _y)*ldf + X_IDX_AOSOA(2, 4)] = smats_v[(0*_ny + _y)*ldsmats +
> X_IDX_AOSOA(0, 2)]*ftemp[0][2] + smats_v[(0*_ny + _y)*ldsmats +
> X_IDX_AOSOA(1, 2)]*ftemp[1][2];\n f_v[(0*_ny + _y)*ldf + X_IDX_AOSOA(3,
> 4)] = smats_v[(0*_ny + _y)*ldsmats + X_IDX_AOSOA(0, 2)]*ftemp[0][3] +
> smats_v[(0*_ny + _y)*ldsmats + X_IDX_AOSOA(1, 2)]*ftemp[1][3];\n
> f_v[(1*_ny + _y)*ldf + X_IDX_AOSOA(0, 4)] = smats_v[(1*_ny + _y)*ldsmats +
> X_IDX_AOSOA(0, 2)]*ftemp[0][0] + smats_v[(1*_ny + _y)*ldsmats +
> X_IDX_AOSOA(1, 2)]*ftemp[1][0];\n f_v[(1*_ny + _y)*ldf + X_IDX_AOSOA(1,
> 4)] = smats_v[(1*_ny + _y)*ldsmats + X_IDX_AOSOA(0, 2)]*ftemp[0][1] +
> smats_v[(1*_ny + _y)*ldsmats + X_IDX_AOSOA(1, 2)]*ftemp[1][1];\n
> f_v[(1*_ny + _y)*ldf + X_IDX_AOSOA(2, 4)] = smats_v[(1*_ny + _y)*ldsmats +
> X_IDX_AOSOA(0, 2)]*ftemp[0][2] + smats_v[(1*_ny + _y)*ldsmats +
> X_IDX_AOSOA(1, 2)]*ftemp[1][2];\n f_v[(1*_ny + _y)*ldf + X_IDX_AOSOA(3,
> 4)] = smats_v[(1*_ny + _y)*ldsmats + X_IDX_AOSOA(0, 2)]*ftemp[0][3] +
> smats_v[(1*_ny + _y)*ldsmats + X_IDX_AOSOA(1, 2)]*ftemp[1][3];\n\n
> }\n }\n }\n
> #undef X_IDX\n #undef X_IDX_AOSOA\n
> }\n\nq\x01]q\x02(cnumpy\nint32\nq\x03h\x03cnumpy\nint64\nq\x04h\x03h\x04h\x03h\x04h\x03e\x87q\x05.',
>
> b'\x80\x03}q\x00.')
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File "/op/anaconda3/bin/pyfr", line 11, in <module>
> load_entry_point('pyfr==1.5.0', 'console_scripts', 'pyfr')()
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/__main__.py",
>
> line 110, in main
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/__main__.py",
>
> line 235, in process_run
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/__main__.py",
>
> line 216, in _process_common
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/solvers/__init__.py",
>
> line 14, in get_solver
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/integrators/__init__.py",
>
> line 43, in get_integrator
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/integrators/std/controllers.py",
>
> line 12, in __init__
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/integrators/std/steppers.py",
>
> line 8, in __init__
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/integrators/std/base.py",
>
> line 12, in __init__
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/integrators/base.py",
>
> line 59, in __init__
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/solvers/base/system.py",
>
> line 65, in __init__
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/solvers/base/system.py",
>
> line 174, in _gen_kernels
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/solvers/euler/elements.py",
>
> line 74, in <lambda>
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/backends/base/backend.py",
>
> line 166, in kernel
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/backends/base/kernels.py",
>
> line 161, in kernel_meth
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/util.py",
>
> line 34, in __call__
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/backends/openmp/provider.py",
>
> line 13, in _build_kernel
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/backends/openmp/compiler.py",
>
> line 61, in __init__
> File
> "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/backends/openmp/compiler.py",
>
> line 33, in __init__
> File "/op/anaconda3/lib/python3.5/ctypes/__init__.py", line 347, in
> __init__
> self._handle = _dlopen(self._name, mode)
> OSError: /op/anaconda3/bin/../lib/libgomp.so.1: version `GOMP_4.0' not
> found (required by /tmp/pyfr-0-i5qtiki9/libtmp.so)
>
> It seems a conflict of GOMP libs. how to resolve this problem? I tried to
> use follow method to diagnose it
>
> [root@localhost couette_flow_2d]# ldd /tmp/pyfr-0-c6hurolh/libtmp.so
> ldd: /tmp/pyfr-0-c6hurolh/libtmp.so: No such file or directory
>
> But the temporary file is missing.
>
> Is there anyway to solve this problem? Is cflags in [backend-openmp]
> helpful to this kind of problem?
>
--
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