Compilation error of Cython #372

JunBlairGeng · 2023-02-22T01:42:51Z

JunBlairGeng
Feb 22, 2023

I just started using pysph last week. I managed to install pysph on MacOS in a conda environment. I pass the tests and am able to run the examples suggested on the installation page. However, recently I was running a code written by my colleague and went into a compilation error. I searched the keywords in the following error information but could not find a solution. However, the same code could be successfully run on my colleague's MacOS.

ERROR

warning: /Users/blair/pysph/pysph/base/nnps_base.pxd:27:13: 'INT_MAX' redeclared
warning: /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:595:21: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:595:27: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:596:25: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:596:37: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:596:50: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:596:65: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:917:23: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:917:32: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1188:24: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1188:37: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.

Error compiling Cython file:
...
for i in range(9):
d_sigma[9d_idx + i] += ms_sigma[9*s_idx + i]WIJ / (rhowsum)

    if self.debug_bound and d_gid[d_idx] == self.debug_bound:
        printf("\n")
        printf("%s\n", "====== Called Boundary Stress ======")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:360:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_sigma[9d_idx + i] += ms_sigma[9*s_idx + i]WIJ / (rhowsum)

    if self.debug_bound and d_gid[d_idx] == self.debug_bound:
        printf("\n")
        printf("%s\n", "====== Called Boundary Stress ======")
        printf("%s\n", "Neighbors")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:361:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%s\n", "====== Called Boundary Stress ======")
printf("%s\n", "Neighbors")
printf("%d\n", s_gid[s_idx])
printf("%d\n", d_gid[d_idx])
printf("\n")
printf("%s\n", "W")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:365:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%d\n", d_gid[d_idx])
printf("\n")
printf("%s\n", "W")
printf("%.9f \n", WIJ)
printf("\n")
printf("%s\n", "Sigma_s")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:368:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
s_sigma[9s_idx + 4],
s_sigma[9s_idx + 5])
printf("%.9f %.9f %.9f\n", s_sigma[9s_idx + 6],
s_sigma[9s_idx + 7],
s_sigma[9*s_idx + 8])
printf('%s\n', "====================================")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:377:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf('%s\n', "====================================")

cdef inline void post_loop(self, long d_idx, double* d_sigma, unsigned int* d_gid):
    if self.debug_bound and d_gid[d_idx] == self.debug_bound:
        printf("\n")
        printf("%s\n", "====== Final Boundary Stress ======")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:382:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...

cdef inline void post_loop(self, long d_idx, double* d_sigma, unsigned int* d_gid):
    if self.debug_bound and d_gid[d_idx] == self.debug_bound:
        printf("\n")
        printf("%s\n", "====== Final Boundary Stress ======")
        printf("%s\n", 'Boundary stress - Sigma')
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:383:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_sigma[9d_idx + 1], d_sigma[9d_idx + 2])
printf("%.16e %.16e %.16e\n", d_sigma[9d_idx + 3],
d_sigma[9d_idx + 4], d_sigma[9d_idx + 5])
printf("%.16e %.16e %.16e\n", d_sigma[9d_idx + 6],
d_sigma[9d_idx + 7], d_sigma[9d_idx + 8])
printf('%s\n', "====================================")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:390:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_eps_dot[9d_idx + 3i + j] += 0.5*(gv_ij + gv_ji)
d_spin_dot[9d_idx + 3i + j] += 0.5*(gv_ij - gv_ji)

    if d_gid[d_idx] == self.debug and self.debug:
        printf("\n")
        printf("%s\n", "====== Called DeformationRates ======")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:445:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_spin_dot[9d_idx + 3i + j] += 0.5*(gv_ij - gv_ji)

    if d_gid[d_idx] == self.debug and self.debug:
        printf("\n")
        printf("%s\n", "====== Called DeformationRates ======")
        printf("%s\n", "Neighbors")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:446:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%s\n", "====== Called DeformationRates ======")
printf("%s\n", "Neighbors")
printf("%d %d\n", d_gid[d_idx], s_gid[s_idx])
printf("\n")

        printf("%s\n", 'Relative particle velocity')
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:450:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...

        printf("%s\n", 'Relative particle velocity')
        printf("%.9f %.9f %.9f\n", VIJ[0], VIJ[1], VIJ[2])
        printf("\n")

        printf("%s\n", "rhoj")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:454:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...

        printf("%s\n", "rhoj")
        printf("%.6f\n", s_rho[s_idx])
        printf("\n")

        printf("%s\n", 'DWIJ')
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:458:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...

        printf("%s\n", 'DWIJ')
        printf("%.9f %.9f %.9f\n", DWIJ[0], DWIJ[1], DWIJ[2])
        printf("\n")

        printf("%s\n", 'Gradient of v')
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:462:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%.16e %.16e %.16e\n", grad_v[0], grad_v[1], grad_v[2])
printf("%.16e %.16e %.16e\n", grad_v[3], grad_v[4], grad_v[5])
printf("%.16e %.16e %.16e\n", grad_v[6], grad_v[7], grad_v[8])
printf('\n')

        printf("%s\n", 'Strain Rate, eps_dot')
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:468:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_eps_dot[9d_idx + 4], d_eps_dot[9d_idx + 5])
printf("%.16e %.16e %.16e\n", d_eps_dot[9d_idx + 6],
d_eps_dot[9d_idx + 7], d_eps_dot[9*d_idx + 8])
printf('\n')

        printf("%s\n", 'Spin Rate, omega_dot')
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:477:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_spin_dot[9d_idx + 1], d_spin_dot[9d_idx + 2])
printf("%.16e %.16e %.16e\n", d_spin_dot[9d_idx + 3],
d_spin_dot[9d_idx + 4], d_spin_dot[9d_idx + 5])
printf("%.16e %.16e %.16e\n", d_spin_dot[9d_idx + 6],
d_spin_dot[9d_idx + 7], d_spin_dot[9d_idx + 8])
printf('%s\n', "=========================")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:484:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
div_vij = VIJ[0]*DWIJ[0] + VIJ[1]*DWIJ[1] + VIJ[2]*DWIJ[2]
d_arho[d_idx] += s_m[s_idx]*div_vij

    if d_gid[d_idx] == self.debug:
        printf("\n")
        printf("%s\n", "====== Called Density Update ======")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:514:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_arho[d_idx] += s_m[s_idx]*div_vij

    if d_gid[d_idx] == self.debug:
        printf("\n")
        printf("%s\n", "====== Called Density Update ======")
        printf("%s\n", "Neighbors")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:515:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%s\n", "====== Called Density Update ======")
printf("%s\n", "Neighbors")
printf("%d\n", s_gid[s_idx])
printf("%d\n", d_gid[d_idx])
printf("\n")
printf("%s\n", "DW")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:519:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%d\n", d_gid[d_idx])
printf("\n")
printf("%s\n", "DW")
printf("%.9f %.9f %.9f\n", DWIJ[0], DWIJ[1], DWIJ[2])
printf("\n")
printf("%s\n", "vij")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:522:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%.9f %.9f %.9f\n", DWIJ[0], DWIJ[1], DWIJ[2])
printf("\n")
printf("%s\n", "vij")
printf("%.9f %.9f %.9f\n", VIJ[0], VIJ[1], VIJ[2])
printf("\n")
printf("%s\n", "d_rho")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:525:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%s\n", "vij")
printf("%.9f %.9f %.9f\n", VIJ[0], VIJ[1], VIJ[2])
printf("\n")
printf("%s\n", "d_rho")
printf("%.9f\n", d_arho[d_idx])
printf('%s\n', "====================================")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:527:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf('%s\n', "====================================")

cdef inline void post_loop(self, long d_idx, unsigned int* d_gid, double* d_arho):
    if self.debug and d_gid[d_idx] == self.debug:
        printf("\n")
        printf("%s\n", "====== Final Density ======")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:532:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...

cdef inline void post_loop(self, long d_idx, unsigned int* d_gid, double* d_arho):
    if self.debug and d_gid[d_idx] == self.debug:
        printf("\n")
        printf("%s\n", "====== Final Density ======")
        printf("%s\n", "Particle")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:533:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("\n")
printf("%s\n", "====== Final Density ======")
printf("%s\n", "Particle")
printf("%d\n", d_gid[d_idx])
printf("\n")
printf("%s\n", "Density rate")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:536:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%s\n", "Particle")
printf("%d\n", d_gid[d_idx])
printf("\n")
printf("%s\n", "Density rate")
printf("%.6f\n", d_arho[d_idx])
printf('%s\n', "====================================")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:538:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
# Flag particle to update stress and strain
d_flag[d_idx] = 1

            if self.debug and d_gid[d_idx] == self.debug:
                printf("\n")
                printf("%s\n", "====== Called DPSolver ======")
                              ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:763:35: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_flag[d_idx] = 1

            if self.debug and d_gid[d_idx] == self.debug:
                printf("\n")
                printf("%s\n", "====== Called DPSolver ======")
                printf("%s\n", 'p trial')
                              ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:764:35: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("\n")
printf("%s\n", "====== Called DPSolver ======")
printf("%s\n", 'p trial')
printf("%.16f\n", d_p[d_idx])
printf('\n')
printf("%s\n", 'q trial')
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:767:35: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf('\n')
printf("%s\n", 'q trial')
printf("%.16f\n", d_q[d_idx])
printf('\n')

                printf("%s\n", 'Sy_n+1,tr')
                              ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:771:35: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf('\n')

                printf("%s\n", 'Sy_n+1,tr')
                printf("%.16f\n", sy)
                printf('\n')
                printf("%s\n", 'Sy_n+1')
                              ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:774:35: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%.16f\n", sy)
printf('\n')
printf("%s\n", 'Sy_n+1')
printf("%.16f\n", d_sy[d_idx])
printf('\n')
printf("%s\n", 'aphi, apsi, ac, acsy, acsy/aphi')
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:777:35: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%s\n", 'aphi, apsi, ac, acsy, acsy/aphi')
printf("%.6f %.6f %.6f %.6f %.9f\n", aphi, apsi, ac, acsy,
acsy/aphi)
printf('\n')

                printf("%s\n", 'Y_tr')
                              ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:782:35: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
norm_s2 += s_i * s_i
d_q[d_idx] = sqrt(3*norm_s2 / 2)

    if self.debug and d_gid[d_idx] == self.debug:

        printf("%s\n", "Stress rate")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:813:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_sigma_dot[idx + 4], d_sigma_dot[idx + 5])
printf("%.6f %.6f %.6f\n", d_sigma_dot[idx + 6],
d_sigma_dot[idx + 7], d_sigma_dot[idx + 8])
printf("\n")

        printf("%s\n", "Plastic strain rate")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:822:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_eps_p_dot[idx + 2])
printf("%.6f %.6f %.6f\n", d_eps_p_dot[idx + 3],
d_eps_p_dot[idx + 4], d_eps_p_dot[idx + 5])
printf("%.6f %.6f %.6f\n", d_eps_p_dot[idx + 6],
d_eps_p_dot[idx + 7], d_eps_p_dot[idx + 8])
printf('%s\n', "====================================")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:829:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
for j in range(n):
d_m_mat[9d_idx + 3i + j] -= v*dwij[i]*xij[j]

        if self.debug and d_gid[d_idx] == self.debug:
            printf("\n")
            printf("%s\n", 'L matrix')
                          ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:942:31: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
if d_wsum[d_idx] == 0.0:
d_wsum[d_idx] = 1.0

    if self.debug and d_gid[d_idx] == self.bound_part:
        printf("\n")
        printf("%s\n", 'Boundary kernel sum')
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:982:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_av[d_idx] += dvdt[1]
d_aw[d_idx] += dvdt[2]

    if d_gid[d_idx] == self.debug:
        printf("\n")
        printf("%s\n", "====== Called MomentumEquation ======")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1037:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_aw[d_idx] += dvdt[2]

    if d_gid[d_idx] == self.debug:
        printf("\n")
        printf("%s\n", "====== Called MomentumEquation ======")
        printf("%s\n", "Neighbors")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1038:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%s\n", "====== Called MomentumEquation ======")
printf("%s\n", "Neighbors")
printf("%d\n", s_gid[s_idx])
printf("%d\n", d_gid[d_idx])
printf("\n")
printf("%s\n", "DW")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1042:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%d\n", d_gid[d_idx])
printf("\n")
printf("%s\n", "DW")
printf("%.9f %.9f %.9f\n", DWIJ[0], DWIJ[1], DWIJ[2])
printf("\n")
printf("%s\n", "Sigma_d")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1045:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_sigma[9d_idx + 5])
printf("%.9f %.9f %.9f\n", d_sigma[9d_idx + 6],
d_sigma[9d_idx + 7],
d_sigma[9d_idx + 8])
printf("\n")
printf("%s\n", "Sigma_s")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1055:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
s_sigma[9 * s_idx + 4],
s_sigma[9 * s_idx + 5])
printf("%.9f %.9f %.9f\n", s_sigma[9 * s_idx + 6],
s_sigma[9 * s_idx + 7],
s_sigma[9 * s_idx + 8])
printf('%s\n', "====================================")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1065:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
# Update total energy
d_te[d_idx] += d_se[d_idx]

    if self.debug and d_gid[d_idx] == self.debug:
        printf("\n")
        printf("%s\n", "====== Final accelerations ======")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1081:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...

    if self.debug and d_gid[d_idx] == self.debug:
        printf("\n")
        printf("%s\n", "====== Final accelerations ======")
        printf("%.9f %.9f %.9f\n", d_au[d_idx], d_av[d_idx], d_aw[d_idx])
        printf('%s\n', "====================================")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1083:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_av[d_idx] += m_pDWIJ[1]
d_aw[d_idx] += m_pDWIJ[2]

            if self.debug and d_gid[d_idx] == self.debug:
                printf("\n")
                printf("%s\n", "====== Called ArtVisc ======")
                              ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1137:35: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("m_p: %.6f\n", s_m[s_idx] * piij)
printf("rho_ij: %.6f\n", 1/RHOIJ1)
printf("alpha: %.6f\n", self.alpha)
printf("beta: %.6f\n", self.beta)
printf("c0: %.6f\n", cij)
printf("%s\n", "DW")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1150:35: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("alpha: %.6f\n", self.alpha)
printf("beta: %.6f\n", self.beta)
printf("c0: %.6f\n", cij)
printf("%s\n", "DW")
printf("%.9f %.9f %.9f\n", DWIJ[0], DWIJ[1], DWIJ[2])
printf('%s\n', "====================================")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1152:35: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...

cdef inline void post_loop(self, long d_idx, double* d_au, double* d_av, double* d_aw, unsigned int* d_gid):
    if self.debug and d_gid[d_idx] == self.debug and (self.alpha != 0.0 or
                                                      self.beta != 0.0):
        printf("\n")
        printf("%s\n", "=== Acceleration with artificial viscosity ===")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1158:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
if self.debug and d_gid[d_idx] == self.debug and (self.alpha != 0.0 or
self.beta != 0.0):
printf("\n")
printf("%s\n", "=== Acceleration with artificial viscosity ===")
printf("%.9f %.9f %.9f\n", d_au[d_idx], d_av[d_idx], d_aw[d_idx])
printf('%s\n', "====================================")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1160:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_sigma_tr[9d_idx + i] = d_sigma[9d_idx + i] + dsigdt
d_sigma_dot[9d_idx + i] = dsig

    if self.debug and d_gid[d_idx] == self.debug:
        printf("\n")
        printf("%s\n", "====== Called TrialStress ======")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1218:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_sigma_dot[9*d_idx + i] = dsig

    if self.debug and d_gid[d_idx] == self.debug:
        printf("\n")
        printf("%s\n", "====== Called TrialStress ======")
        printf("%s\n", "Sigma trial")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1219:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%.6f %.6f %.6f\n", d_sigma_tr[9d_idx + 3],
d_sigma_tr[9d_idx + 4], d_sigma_tr[9d_idx + 5])
printf("%.6f %.6f %.6f\n", d_sigma_tr[9d_idx + 6],
d_sigma_tr[9d_idx + 7], d_sigma_tr[9d_idx + 8])
printf("\n")
printf("%s\n", "Sigma dot")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1227:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_sigma_dot[9d_idx + 1], d_sigma_dot[9d_idx + 2])
printf("%.6f %.6f %.6f\n", d_sigma_dot[9d_idx + 3],
d_sigma_dot[9d_idx + 4], d_sigma_dot[9d_idx + 5])
printf("%.6f %.6f %.6f\n", d_sigma_dot[9d_idx + 6],
d_sigma_dot[9d_idx + 7], d_sigma_dot[9d_idx + 8])
printf('%s\n', "====================================")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1234:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...

    d_q[d_idx] = sqrt(3.0*s2 / 2.0)

    if self.debug and d_gid[d_idx] == self.debug:
        printf("\n")
        printf("%s\n", '=== Called StressDecomposition ===')
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1278:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_q[d_idx] = sqrt(3.0*s2 / 2.0)

    if self.debug and d_gid[d_idx] == self.debug:
        printf("\n")
        printf("%s\n", '=== Called StressDecomposition ===')
        printf("%s\n", 'p')
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1279:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("\n")
printf("%s\n", '=== Called StressDecomposition ===')
printf("%s\n", 'p')
printf("%.6f\n", p)
printf("\n")
printf("%s\n", 'q')
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1282:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%s\n", 'p')
printf("%.6f\n", p)
printf("\n")
printf("%s\n", 'q')
printf("%.6f\n", d_q[d_idx])
printf('%s\n', "====================================")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1284:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_z[d_idx] += coef*VIJ[2]*dt

cdef inline void post_loop(self, long d_idx, double* d_x, double* d_y, double* d_z, unsigned int* d_gid):
    if self.debug and d_gid[d_idx] == self.debug and self.eps > 0.0:
        printf("\n")
        printf("%s\n", "=== New velocities after XSPH correction ===")
                      ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1324:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
cdef inline void post_loop(self, long d_idx, double* d_x, double* d_y, double* d_z, unsigned int* d_gid):
if self.debug and d_gid[d_idx] == self.debug and self.eps > 0.0:
printf("\n")
printf("%s\n", "=== New velocities after XSPH correction ===")
printf("%.9f %.9f %.9f\n", d_x[d_idx], d_y[d_idx], d_z[d_idx])
printf('%s\n', "====================================")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:1326:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("\n")
printf("Updated position: %.9f %.9f %.9f\n", d_x[d_idx],
d_y[d_idx], d_z[d_idx])
printf("Updated velocity: %.9f %.9f %.9f\n", d_u[d_idx],
d_v[d_idx], d_w[d_idx])
printf("%s\n", "Updated stress")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:2904:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
d_sigma[9d_idx + 2])
printf("%.9f %.9f %.9f\n", d_sigma[9d_idx + 3],
d_sigma[9d_idx + 4], d_sigma[9d_idx + 5])
printf("%.9f %.9f %.9f\n", d_sigma[9d_idx + 6],
d_sigma[9d_idx + 7], d_sigma[9*d_idx + 8])
printf("%s\n", 'p')
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:2911:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%.9f %.9f %.9f\n", d_sigma[9d_idx + 6],
d_sigma[9d_idx + 7], d_sigma[9*d_idx + 8])
printf("%s\n", 'p')
printf("%.9f\n", d_p[d_idx])
printf("\n")
printf("%s\n", 'q')
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:2914:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%.9f\n", d_p[d_idx])
printf("\n")
printf("%s\n", 'q')
printf("%.9f\n", d_q[d_idx])
printf("\n")
printf("%s\n", "Updated strain")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:2917:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%.9f %.9f %.9f\n", d_eps[9 * d_idx + 3],
d_eps[9 * d_idx + 4], d_eps[9 * d_idx + 5])
printf("%.9f %.9f %.9f\n", d_eps[9 * d_idx + 6],
d_eps[9 * d_idx + 7], d_eps[9 * d_idx + 8])
printf("\n")
printf("%s\n", "Plastic strain")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:2925:27: Python object cannot be passed as a varargs parameter

Error compiling Cython file:

...
printf("%.9f %.9f %.9f\n", d_eps_p[9 * d_idx + 3],
d_eps_p[9 * d_idx + 4], d_eps_p[9 * d_idx + 5])
printf("%.9f %.9f %.9f\n", d_eps_p[9 * d_idx + 6],
d_eps_p[9 * d_idx + 7], d_eps_p[9 * d_idx + 8])
printf("\n")
printf("%s\n", "Elastic strain")
^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.pyx:2933:27: Python object cannot be passed as a varargs parameter
/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_c19b0920dc3337a73a8894d8ced774d0.cpp:1:2: error: Do not use this file, it is the result of a failed Cython compilation.
#error Do not use this file, it is the result of a failed Cython compilation.
^
1 error generated.

Answered by prabhuramachandran

Feb 22, 2023

This is Cython and not C so there are some subtle differences. If you see the error message, all your errors are with the printf statement you have added, and not with anything else. Try this:

printf("Elastic strain\n")

The problem is when you pass "%s" and the argument of "Elastic strain", in this case the second is a Python object (a string) and this cannot be passed as an argument directly to the C function printf. Since all you want is a string to be printed, just calling printf("string") will work. For other integer and number arguments the usual printf("%f\n", some_float) will work fine.

View full answer

prabhuramachandran · 2023-02-22T03:07:17Z

prabhuramachandran
Feb 22, 2023
Maintainer

This is Cython and not C so there are some subtle differences. If you see the error message, all your errors are with the printf statement you have added, and not with anything else. Try this:

printf("Elastic strain\n")

The problem is when you pass "%s" and the argument of "Elastic strain", in this case the second is a Python object (a string) and this cannot be passed as an argument directly to the C function printf. Since all you want is a string to be printed, just calling printf("string") will work. For other integer and number arguments the usual printf("%f\n", some_float) will work fine.

0 replies

JunBlairGeng · 2023-02-23T01:28:59Z

JunBlairGeng
Feb 23, 2023
Author

Hi Prabhu,

Thanks for the advice! I deleted all the "%s" in the code. However, it still gives me the same error message. Also, I find that I don't have these

printf("%s\n", "Elastic strain")

things in my code.

Also, in the error message, it seems that the error is in the temporary file .pysph/source/py3.7-macosx-10.9-x86_64/m_82019ae34e4c02317b6781d8ce2df9c4.pyx:2933:27.

Error compiling Cython file:

            printf("%.9f %.9f %.9f\n", d_eps_p[9 * d_idx + 3],
                   d_eps_p[9 * d_idx + 4], d_eps_p[9 * d_idx + 5])
            printf("%.9f %.9f %.9f\n", d_eps_p[9 * d_idx + 6],
                   d_eps_p[9 * d_idx + 7], d_eps_p[9 * d_idx + 8])
            printf("\n")
            printf("%s\n", "Elastic strain")
                          ^

/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_82019ae34e4c02317b6781d8ce2df9c4.pyx:2933:27: Python object cannot be passed as a varargs parameter

As I searched for this file, the sd_pysph.log popped up (The filename of the code I'm running is sd_pysph.py):

INFO|2023-02-22 17:12:31,351|pysph.solver.application|Started as:
sd_pysph.py --pfreq=100 --c_model=1 --y_criterion=2 --kernel-grad-correct=1 --kernel=WendlandQuintic --gravity=-9.8
INFO|2023-02-22 17:12:31,352|pysph.solver.application|Running on DN0a2454b0.SUNet with address 10.36.84.176
INFO|2023-02-22 17:12:31,352|pysph.solver.application|Using OpenMP schedule dynamic,64
INFO|2023-02-22 17:12:31,565|pysph.solver.application|Generating output in /Users/blair/pysph/pysph/GEOSPH_stable_Blair2/sd_pysph_output
INFO|2023-02-22 17:12:31,705|compyle.ext_module|Compiling code at: /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_82019ae34e4c02317b6781d8ce2df9c4.pyx
DEBUG|2023-02-22 17:12:31,732|root|No `name` configuration, performing automatic discovery
INFO|2023-02-22 17:12:31,732|root|running build_ext
INFO|2023-02-22 17:12:31,870|root|cythoning /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_82019ae34e4c02317b6781d8ce2df9c4.pyx to /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_82019ae34e4c02317b6781d8ce2df9c4.cpp
INFO|2023-02-22 17:12:32,993|root|building 'm_82019ae34e4c02317b6781d8ce2df9c4' extension
INFO|2023-02-22 17:12:32,993|root|gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/blair/opt/anaconda3/envs/pysph_env2/include -arch x86_64 -I/Users/blair/opt/anaconda3/envs/pysph_env2/include -arch x86_64 -I/Users/blair/opt/anaconda3/envs/pysph_env2/lib/python3.7/site-packages/numpy/core/include -I/Users/blair/pysph/pysph/base -I/Users/blair/opt/anaconda3/envs/pysph_env2/include/python3.7m -c /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_82019ae34e4c02317b6781d8ce2df9c4.cpp -o /Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/build/temp.macosx-10.9-x86_64-cpython-37/Users/blair/.pysph/source/py3.7-macosx-10.9-x86_64/m_82019ae34e4c02317b6781d8ce2df9c4.o

0 replies

prabhuramachandran · 2023-02-23T03:42:07Z

prabhuramachandran
Feb 23, 2023
Maintainer

Those files are automatically generated from your equations. So you must have those print statements in some equation you are using. You can read the file ~/.pysph/source/py3.7-macosx-10.9-x86_64/m_82019ae34e4c02317b6781d8ce2df9c4.pyx and see which specific equation that is, if you want, it is just a cython file.

2 replies

JunBlairGeng Feb 23, 2023
Author

Thanks!

I found the file and managed to find where else I didn't fully delete the "%s" statement.

The code finally works! Thanks again for your time and help!

JunBlairGeng Feb 23, 2023
Author

Hi Prabhu,

Sorry to bother you again. I'm just being curious. Why could my colleague run this code without doing the modifications but I couldn't? Is it due to the different cython package version or what?

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