Issue with polytrope file

Bug/problem reports for any of the GYRE executables (gyre_ad, gyre_nad, etc)
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Ippocratis Saltas
Posts: 8
Joined: Mon May 21, 2018 9:09 am

Issue with polytrope file

Post by Ippocratis Saltas » Sun May 27, 2018 3:39 pm

Hi,

Let me apologise in advance for the possibly naive question -- Let me know if it doesn't fit in this section.

I am trying to use my own polytropic file, which I produce running a short python script. I include all attributes according to the convention of the original files (\Gamma_1, n_d ... ), along with the data points for \Theta, \dTheta and \xi, but I seem to get an error when running the gyre code (on an OS X). Please see the terminal's output below.

I understand there is some issue with the way I am producing the file, but can't trace it.

Thank you in advance.

---
HDF5-DIAG: Error detected in HDF5 (1.8.17) thread 0:
#000: H5F.c line 604 in H5Fopen(): unable to open file
major: File accessibilty
minor: Unable to open file
#001: H5Fint.c line 1091 in H5F_open(): unable to read root group
major: File accessibilty
minor: Unable to open file
#002: H5Groot.c line 241 in H5G_mkroot(): can't check if symbol table message exists
major: Symbol table
minor: Can't get value
#003: H5Omessage.c line 888 in H5O_msg_exists(): unable to protect object header
major: Object header
minor: Unable to protect metadata
#004: H5O.c line 1685 in H5O_protect(): unable to load object header
major: Object header
minor: Unable to protect metadata
#005: H5AC.c line 1262 in H5AC_protect(): H5C_protect() failed.
major: Object cache
minor: Unable to protect metadata
#006: H5C.c line 3574 in H5C_protect(): can't load entry
major: Object cache
minor: Unable to load metadata into cache
#007: H5C.c line 7954 in H5C_load_entry(): unable to load entry
major: Object cache
minor: Unable to load metadata into cache
#008: H5Ocache.c line 275 in H5O_load(): bad object header version number
major: Object header
minor: Wrong version number
HDF5-DIAG: Error detected in HDF5 (1.8.17) thread 0:
#000: H5F.c line 604 in H5Fopen(): unable to open file
major: File accessibilty
minor: Unable to open file
#001: H5Fint.c line 1091 in H5F_open(): unable to read root group
major: File accessibilty
minor: Unable to open file
#002: H5Groot.c line 241 in H5G_mkroot(): can't check if symbol table message exists
major: Symbol table
minor: Can't get value
#003: H5Omessage.c line 888 in H5O_msg_exists(): unable to protect object header
major: Object header
minor: Unable to protect metadata
#004: H5O.c line 1685 in H5O_protect(): unable to load object header
major: Object header
minor: Unable to protect metadata
#005: H5AC.c line 1262 in H5AC_protect(): H5C_protect() failed.
major: Object cache
minor: Unable to protect metadata
#006: H5C.c line 3574 in H5C_protect(): can't load entry
major: Object cache
minor: Unable to load metadata into cache
#007: H5C.c line 7954 in H5C_load_entry(): unable to load entry
major: Object cache
minor: Unable to load metadata into cache
#008: H5Ocache.c line 275 in H5O_load(): bad object header version number
major: Object header
minor: Wrong version number
ABORT at line 388 <core_hgroup:init_file_>:
Error in call to h5fopen_f
STOP Program aborted

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rhtownsend
Site Admin
Posts: 281
Joined: Sun Mar 31, 2013 4:22 pm

Re: Issue with polytrope file

Post by rhtownsend » Sun May 27, 2018 3:41 pm

Ippocratis Saltas wrote:
Sun May 27, 2018 3:39 pm
Hi,

Let me apologise in advance for the possibly naive question -- Let me know if it doesn't fit in this section.

I am trying to use my own polytropic file, which I produce running a short python script. I include all attributes according to the convention of the original files (\Gamma_1, n_d ... ), along with the data points for \Theta, \dTheta and \xi, but I seem to get an error when running the gyre code (on an OS X). Please see the terminal's output below.

I understand there is some issue with the way I am producing the file, but can't trace it.

Thank you in advance.

---
HDF5-DIAG: Error detected in HDF5 (1.8.17) thread 0:
#000: H5F.c line 604 in H5Fopen(): unable to open file
major: File accessibilty
minor: Unable to open file
#001: H5Fint.c line 1091 in H5F_open(): unable to read root group
major: File accessibilty
minor: Unable to open file
#002: H5Groot.c line 241 in H5G_mkroot(): can't check if symbol table message exists
major: Symbol table
minor: Can't get value
#003: H5Omessage.c line 888 in H5O_msg_exists(): unable to protect object header
major: Object header
minor: Unable to protect metadata
#004: H5O.c line 1685 in H5O_protect(): unable to load object header
major: Object header
minor: Unable to protect metadata
#005: H5AC.c line 1262 in H5AC_protect(): H5C_protect() failed.
major: Object cache
minor: Unable to protect metadata
#006: H5C.c line 3574 in H5C_protect(): can't load entry
major: Object cache
minor: Unable to load metadata into cache
#007: H5C.c line 7954 in H5C_load_entry(): unable to load entry
major: Object cache
minor: Unable to load metadata into cache
#008: H5Ocache.c line 275 in H5O_load(): bad object header version number
major: Object header
minor: Wrong version number
HDF5-DIAG: Error detected in HDF5 (1.8.17) thread 0:
#000: H5F.c line 604 in H5Fopen(): unable to open file
major: File accessibilty
minor: Unable to open file
#001: H5Fint.c line 1091 in H5F_open(): unable to read root group
major: File accessibilty
minor: Unable to open file
#002: H5Groot.c line 241 in H5G_mkroot(): can't check if symbol table message exists
major: Symbol table
minor: Can't get value
#003: H5Omessage.c line 888 in H5O_msg_exists(): unable to protect object header
major: Object header
minor: Unable to protect metadata
#004: H5O.c line 1685 in H5O_protect(): unable to load object header
major: Object header
minor: Unable to protect metadata
#005: H5AC.c line 1262 in H5AC_protect(): H5C_protect() failed.
major: Object cache
minor: Unable to protect metadata
#006: H5C.c line 3574 in H5C_protect(): can't load entry
major: Object cache
minor: Unable to load metadata into cache
#007: H5C.c line 7954 in H5C_load_entry(): unable to load entry
major: Object cache
minor: Unable to load metadata into cache
#008: H5Ocache.c line 275 in H5O_load(): bad object header version number
major: Object header
minor: Wrong version number
ABORT at line 388 <core_hgroup:init_file_>:
Error in call to h5fopen_f
STOP Program aborted
Hi Ippocratis --

Can you try reading the error message? There is a hint on the second line, which tells you what the problem is.

cheers,

Rich

Ippocratis Saltas
Posts: 8
Joined: Mon May 21, 2018 9:09 am

Re: Issue with polytrope file

Post by Ippocratis Saltas » Sun May 27, 2018 3:59 pm

Hi Rich,

Thanks for your reply.

It seems it can't open the file for some reason -- I have not been sure as to whether there is some subtlety when producing it that is causing it.

Ippocratis Saltas
Posts: 8
Joined: Mon May 21, 2018 9:09 am

Re: Issue with polytrope file

Post by Ippocratis Saltas » Sun May 27, 2018 4:34 pm

Hi Rich

Indeed, there was a bug with my file -- Sorry for the hassle. I still can't make it work though, getting the error below. Do you have any clue as to where I should be looking at?

Thanks.


Mode Search
-----------

Mode parameters
l : 0
m : 0

Building frequency scan
added scan interval : 0.3000E+01 -> 0.1420E+02 (30 points, LINEAR)

Building x grid
Found inner turning points, x range 0.0488 -> 0.1277
Adding 0 global point(s) in iteration 1
Final grid has 1 segment(s) and 1001 point(s):
Segment 1 : x range 0.0000 -> 1.0000 (1 -> 1001)

ASSERT 'pt_i%x == 0._WP' failed at line 118 <gyre_rad_bound:rad_bound_t_>:
Boundary condition invalid for x /= 0

User avatar
rhtownsend
Site Admin
Posts: 281
Joined: Sun Mar 31, 2013 4:22 pm

Re: Issue with polytrope file

Post by rhtownsend » Sun May 27, 2018 5:41 pm

Ippocratis Saltas wrote:
Sun May 27, 2018 4:34 pm
Hi Rich

Indeed, there was a bug with my file -- Sorry for the hassle. I still can't make it work though, getting the error below. Do you have any clue as to where I should be looking at?

Thanks.


Mode Search
-----------

Mode parameters
l : 0
m : 0

Building frequency scan
added scan interval : 0.3000E+01 -> 0.1420E+02 (30 points, LINEAR)

Building x grid
Found inner turning points, x range 0.0488 -> 0.1277
Adding 0 global point(s) in iteration 1
Final grid has 1 segment(s) and 1001 point(s):
Segment 1 : x range 0.0000 -> 1.0000 (1 -> 1001)

ASSERT 'pt_i%x == 0._WP' failed at line 118 <gyre_rad_bound:rad_bound_t_>:
Boundary condition invalid for x /= 0
Hi Ippocratis --

Glad you found the problem!

What this new error means is that the inner-most (first) point in your polytrope does not have x=0. Your options here are to fix your model to start at x=0, or choose a boundary condition that is valid for application at x/=0 (see the documentation for the inner_bound parameter).

cheers,

Rich

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