I have an hdf5 file which was generated by clavis. When I try to open it in octave, I get the following error:
error: load: error while reading hdf5 item decision
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 2964195136:
#000: ../../../src/H5Gdeprec.c line 777 in H5Giterate(): group iteration failed
major: Symbol table
minor: Iteration failed
#001: ../../../src/H5G.c line 1532 in H5G_iterate(): error iterating over links
major: Symbol table
minor: Iteration failed
#002: ../../../src/H5Gobj.c line 599 in H5G_obj_iterate(): can't iterate over symbol table
major: Symbol table
minor: Iteration failed
#003: ../../../src/H5Gstab.c line 522 in H5G_stab_iterate(): iteration operator failed
major: Symbol table
minor: Can't move to next iterator location
#004: ../../../src/H5B.c line 1302 in H5B_iterate(): B-tree iteration failed
major: B-Tree node
minor: Iteration failed
#005: ../../../src/H5B.c line 1225 in H5B_iterate_helper(): iterator function failed
major: B-Tree node
minor: Unable to list node
#006: ../../../src/H5Gnode.c line 1021 in H5G_node_iterate(): iteration operator failed
major: Symbol table
minor: Can't move to next iterator location
How can I find out what's wrong with my file? Or is this a bug in hdf5?
It opens in HDFView, but it still prints out the same error nonetheless
Here's the file: http://www.wikiupload.com/JRGTR40KV2EVR3G
It turns out this is a bug in Octave (or rather a call to a deprecated HDF5 function. I don't know what was going on with HDFView). I created a bug report for it: http://savannah.gnu.org/bugs/?39491
Related
On assignment, they gave me a step-by-step example from this article http://wiki.octave.org/Bim_package.
The example was typed manually, without copy-paste.I already install this packages- fpl, bim,msh, image.
Octave example:
pkg load bim
pkg load msh
pkg load fpl
[mesh]=msh2m_gmsh("fuime","scale",1,"clscale",.1); – Error
[mesh]=bim2c_mesh_properties(mesh);
pdemesh(mesh.p,mesh.e,mesh.t);
view(2)
xu=mesh.p(1,:).';
yu=mesh.p(2,:).';
nelems=columns(mesh.t);
nnodes=columns(mesh.p);
epsilon=.1;
phi=xu+yu;
AdvDiff=bim2a_advaction_diffusion(mesh,epsilon,1,1,phi);
Mass=bim2a_reaction(mesh,1,1);
b=bim2a_rhs(mesh,f,g);
A=AdvDiff+Mass;
GammaD=bim2c_unknowns_on_side(mesh,[1 2]);
GammaN=bim2c_unknowns_on_side(mesh,[3 4]);
GammaN=setdiff(GammaN,GammaD);
jn=zeros(length(GammaN),1);
ud=3*xu;
Omega=setdiff(1:nnodes,union(GammaD,GammaN));
Add=A(GammaD,GammaD);
Adn=A(GammaD,GammaN);
Adi=A(GammaD,Omega);
And=A(GammaN,GammaD);
Ann=A(GammaN,GammaN);
Ani=A(GammaN,Omega);
Aid=A(Omega,GammaD);
Ain=A(Omega,GammaN);
Aii=A(Omega,Omega);
bd=b(GammaD);
bn=b(GammaN);
bi=b(Omega);
temp=[Ann Ani;Ain Aii]\[jn+bn-And*ud(GammaD); bi-Aid*ud(GammaD)];
u=ud;
u(GammaN)=temp(1:numel(GammaN));
u(Omega)=temp(length(GammaN)+1:end);
jd=[Add Adi Adn]*u([GammaD;Omega;GammaN])-bd;
[gx,gy]=bim2c_pde_gradient(mesh,u);
[jxglob,jyglob]=bim2c_global_flux(mesh,u,epsilon*ones(nelems,1),ones(nnodes,1),ones(nnodes,1),phi);
fpl_vtk_write_field("vtkdata",mesh,{u,"Solution"},{[gx:gy]',"Gradient"},1);
pdesurf(mesh.p,mesh.t,u);
In this - [mesh]=msh2m_gmsh("fuime","scale",1,"clscale",.1);Error
Generating mesh...
error: 'tmpnam' undefined near line 78, column 78
error: called from
msh2m_gmsh at line 78 column 12
>>
WHAT HAVE I TAKEN TO FIX THE ERROR
I decided that the problem is in uninstalled packages.
According to the answer I was given in this thread Error,when installing a new package in Octave.
I started to install the package mesh, but here another error came out.
error: get_forge_pkg: package not found: "mesh". Maybe you meant "lssa?"
error: called from
get_forge_pkg at line 90 column 5
get_forge_download at line 32 column 14
pkg at line 500 column 31
But the mesh package not found.The package msh already installed.
How I can fixed my problem?
I am trying to read an input from csv file (input.csv, in the same folder of this f95 file) which has some numbers in certain columns. while I execute my program, it gives error
program received signal SIGSEGV: segmentation fault - invalid memory reference. backtrace =#0 ffffffff
the code is below; it terminates after the first print statement.
program section
implicit none
integer::no_num,count_le,count_cve,count_cvx,count_ce
integer::i,j
double precision,allocatable,dimension(:)::x1,y1,x2,y2
double precision,allocatable,dimension(:)::xc,yc,rc,sa,ea
character (2),allocatable,dimension(:):: asc,asl,sd
character(100)::rand_char ! random characters/txt
print*,"program"
open(unit=100,file='input.csv')
print*,"check"
close(100)
end program
I want to iterator the value in xpath /root/filepath in xml_1.xml by using ForEachLoop container in SSIS, see my xml file full path as below:
my XML file content looks like this:
<root>
<filepath>1.txt</filepath>
<filepath>2.txt</filepath>
</root>
and below screenshots are my packages in SSIS:
but when I run this package, I always get following error message:
SSIS package "C:\Users\zhanzhex\source\repos\Integration Services Project1\Integration Services Project1\loopThrowXml.dtsx" starting.
Error: 0xC0010014 at Foreach Loop Container, Foreach NodeList Enumerator: Data at the root level is invalid. Line 1, position 1.
Warning: 0x80019002 at Foreach Loop Container: SSIS Warning Code DTS_W_MAXIMUMERRORCOUNTREACHED. The Execution method succeeded, but the number of errors raised (1) reached the maximum allowed (1); resulting in failure. This occurs when the number of errors reaches the number specified in MaximumErrorCount. Change the MaximumErrorCount or fix the errors.
Warning: 0x80019002 at loopThrowXml: SSIS Warning Code DTS_W_MAXIMUMERRORCOUNTREACHED. The Execution method succeeded, but the number of errors raised (1) reached the maximum allowed (1); resulting in failure. This occurs when the number of errors reaches the number specified in MaximumErrorCount. Change the MaximumErrorCount or fix the errors.
SSIS package "C:\Users\zhanzhex\source\repos\Integration Services Project1\Integration Services Project1\loopThrowXml.dtsx" finished: Failure.
The program '[1168] DtsDebugHost.exe: DTS' has exited with code 0 (0x0).
can anybody tell me why and how to fix it?
I have been following https://github.com/weiliu89/caffe/tree/ssd to get the caffe environment working. I have gotten upto step 3.
The following line of script is throwing exception.. What could be wrong?
./data/VOC0712/create_list.sh
I0101 21:34:28.608160 2648 get_image_size.cpp:105] Processed 4952 files.
*** Error in `/home/ram/project/caffe/data/VOC0712/../../build/tools/get_image_size': free(): invalid pointer: 0x00000000025602c0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fc8422137e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7fc84221c37a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7fc84222053c]
/usr/lib/x86_64-linux-gnu/libprotobuf.so.9(_ZN6google8protobuf8internal28DestroyDefaultRepeatedFieldsEv+0x1f)[0x7fc841ecc8af]
/usr/lib/x86_64-linux-gnu/libprotobuf.so.9(_ZN6google8protobuf23ShutdownProtobufLibraryEv+0x8b)[0x7fc841ecbb3b]
/usr/lib/x86_64-linux-gnu/libmirprotobuf.so.3(+0x233b9)[0x7fc82670e3b9]
/lib64/ld-linux-x86-64.so.2(+0x10de7)[0x7fc843a9cde7]
/lib/x86_64-linux-gnu/libc.so.6(+0x39ff8)[0x7fc8421d5ff8]
/lib/x86_64-linux-gnu/libc.so.6(+0x3a045)[0x7fc8421d6045]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf7)[0x7fc8421bc837]
/home/ram/project/caffe/data/VOC0712/../../build/tools/get_image_size[0x4039d9]
Thanks,
Ram
I could resolve this issue by running under python3 instead of python2.
alias python=python3
When I load Octave each time I get the below errors after the welcome/info message.
error: `prefix' undefined near line 12 column 35
error: evaluating argument list element number 2
error: called from:
error: C:\Octave\Octave3.4.3_gcc4.5.2\share\octave\site\m\startup/octaverc at line 12, column 1
octave:1>
Does anybody know why this is happening?
For that version of octave, the default settings of that file around that line are:
prefix=octave_config_info('prefix');
setenv('path',[getenv('path'),';',prefix,'\mingw32\bin;',prefix,'\msys\bin']);
setenv('path',[getenv('path'),';',prefix,'\gs\gs9.02\bin'])
So you should check if it has changed