ENUM error when running basset_train.lua about basset HOT 7 OPEN

Sounds like an HDF5 compatibility issue. Check out this previous issue #40. Unfortunately, you’ll need to use HDF5 version 1.8 as discussed there.

from basset.

Hi Dave,

Thanks for the response.

I already had HDF5 1.8 installed. To double check I ran h5dump --version and I got h5dump: Version 1.8.12. However, when I start up torch and run require 'hdf5' it gives me something similar to issue #25 (comment). I have attached what I get:

th> require 'hdf5'
{
H5Z_FILTER_CONFIG_ENCODE_ENABLED : 1
H5F_ACC_RDWR : 1
_getTorchType : function: 0x41b2fd18
H5F_OBJ_FILE : 1
H5S_ALL : 0
H5F_OBJ_GROUP : 4
C : userdata: 0x403b21f0
H5P_DEFAULT : 0
_describeObject : function: 0x41dc5718
H5Z_FILTER_NBIT : 5
_debugMode : false
_getObjectType : function: 0x41dc56d8
H5F_OBJ_ALL : 31
_getObjectName : function: 0x41b2fd38
version :
{
1 : 1
2 : 8
3 : 12
}
H5Z_FILTER_SHUFFLE : 2
HDF5Group : {...}
open : function: 0x402b8c50
H5Z_FILTER_SZIP : 4
H5F_OBJ_ATTR : 16
H5Z_FILTER_FLETCHER32 : 3
H5F_OBJ_DATATYPE : 8
debugMode : function: 0x402b8bd0
H5F_ACC_EXCL : 4
H5Z_FILTER_NONE : 0
_testUtils :
{
deepAlmostEq : function: 0x402b8b90
withTmpDir : function: 0x402b8af0
}
_nativeTypeForTensorType : function: 0x41b2fcb0
H5F_ACC_TRUNC : 2
_config :
{
HDF5_INCLUDE_PATH : "/usr/include"
HDF5_LIBRARIES : "/usr/lib64/libhdf5.so;/usr/lib64/libsz.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so"
}
_loadObject : function: 0x402b8c30
DataSetOptions : {...}
HDF5DataSet : {...}
H5Z_FILTER_RESERVED : 256
_logger :
{
error : function: 0x41b86850
warn : function: 0x41b86850
debug : function: 0x41b86898
}
H5F_ACC_RDONLY : 0
_fletcher32Available : function: 0x41dc5738
H5Z_FILTER_CONFIG_DECODE_ENABLED : 2
ffi :
{
abi : function: builtin#202
copy : function: builtin#200
errno : function: builtin#198
typeinfo : function: builtin#193
alignof : function: builtin#196
cdef : function: builtin#189
C : userdata: 0x41b8b398
cast : function: builtin#191
load : function: builtin#205
offsetof : function: builtin#197
sizeof : function: builtin#195
string : function: builtin#199
metatype : function: builtin#203
new : function: builtin#190
arch : "x64"
os : "Linux"
gc : function: builtin#204
fill : function: builtin#201
istype : function: builtin#194
typeof : function: builtin#192
}
H5Z_FILTER_ERROR : -1
_outputTypeForTensorType : function: 0x41b8df30
H5Z_FILTER_MAX : 65535
h5t :
{
STD_B32LE : 50331728
IEEE_F32BE : 50331703
NATIVE_B16 : 50331694
NATIVE_HSIZE : 50331698
NO_CLASS : -1
NATIVE_UINT_FAST32 : 50331681
STD_B8LE : 50331724
STD_I64BE : 50331715
NATIVE_LONG : 50331662
NATIVE_DOUBLE : 50331691
TIME : 2
NATIVE_INT16 : 50331670
NATIVE_LLONG : 50331688
STD_I8BE : 50331709
STD_B64LE : 50331730
NATIVE_HSSIZE : 50331699
STD_B32BE : 50331729
INTEGER : 0
NATIVE_INT64 : 50331682
STD_I8LE : 50331708
STD_I32LE : 50331712
NATIVE_SCHAR : 50331656
NATIVE_INT_FAST16 : 50331674
NATIVE_INT : 50331660
BITFIELD : 4
NATIVE_UINT_LEAST16 : 50331673
NATIVE_INT_LEAST16 : 50331672
IEEE_F64LE : 50331704
NATIVE_INT_FAST64 : 50331686
NATIVE_UINT_FAST64 : 50331687
NATIVE_UINT_LEAST64 : 50331685
NATIVE_INT_LEAST64 : 50331684
ENUM : 8
NATIVE_UINT64 : 50331683
NATIVE_HBOOL : 50331701
NATIVE_ULONG : 50331663
NATIVE_INT_FAST32 : 50331680
NATIVE_HADDR : 50331697
NATIVE_UINT : 50331661
NCLASSES : 11
NATIVE_UINT_LEAST32 : 50331679
NATIVE_INT_LEAST32 : 50331678
STD_U64LE : 50331722
NATIVE_UINT32 : 50331677
NATIVE_SHORT : 50331658
NATIVE_INT32 : 50331676
VLEN : 9
ARRAY : 10
STD_U16LE : 50331718
STD_B16LE : 50331726
STD_I64LE : 50331714
NATIVE_UINT16 : 50331671
NATIVE_UINT_FAST8 : 50331669
STD_B16BE : 50331727
NATIVE_INT_FAST8 : 50331668
FLOAT : 1
REFERENCE : 7
STD_U32LE : 50331720
NATIVE_USHORT : 50331659
NATIVE_ULLONG : 50331689
NATIVE_INT8 : 50331664
IEEE_F32LE : 50331702
STD_U8BE : 50331717
NATIVE_INT_LEAST8 : 50331666
NATIVE_UINT8 : 50331665
NATIVE_B32 : 50331695
NATIVE_HERR : 50331700
NATIVE_OPAQUE : 50331736
NATIVE_LDOUBLE : 50331692
NATIVE_UINT_LEAST8 : 50331667
COMPOUND : 6
STD_REF_OBJ : 50331739
NATIVE_UINT_FAST16 : 50331675
NATIVE_B64 : 50331696
STD_U16BE : 50331719
STD_REF_DSETREG : 50331740
NATIVE_B8 : 50331693
STD_I32BE : 50331713
IEEE_F64BE : 50331705
NATIVE_FLOAT : 50331690
NATIVE_UCHAR : 50331657
STD_U32BE : 50331721
OPAQUE : 5
STD_B64BE : 50331731
STD_U8LE : 50331716
STD_I16BE : 50331711
STD_B8BE : 50331725
STRING : 3
STD_I16LE : 50331710
STD_U64BE : 50331723
}
HDF5File : {...}
H5Z_FILTER_SCALEOFFSET : 6
H5Z_FILTER_DEFLATE : 1
H5F_ACC_CREAT : 16
H5F_UNLIMITED : 18446744073709551615ULL
_deflateAvailable : function: 0x41dc5780
_inDebugMode : function: 0x402b8c10
H5F_OBJ_LOCAL : 32
H5S_SELECT_SET : 0
_datatypeName : function: 0x41541360
H5F_ACC_DEBUG : 8
H5F_OBJ_DATASET : 2
}
[1.3558s]
th> require 'HDF5'
...ainmunirpatel/torch/install/share/lua/5.1/trepl/init.lua:389: module 'HDF5' not found:No LuaRocks module found for HDF5
no field package.preload['HDF5']
no file '/home/hugheslab2/zainmunirpatel/.luarocks/share/lua/5.1/HDF5.lua'
no file '/home/hugheslab2/zainmunirpatel/.luarocks/share/lua/5.1/HDF5/init.lua'
no file '/home/hugheslab2/zainmunirpatel/torch/install/share/lua/5.1/HDF5.lua'
no file '/home/hugheslab2/zainmunirpatel/torch/install/share/lua/5.1/HDF5/init.lua'
no file '/home/hugheslab2/zainmunirpatel/Basset/src/HDF5.lua'
no file './HDF5.lua'
no file '/home/hugheslab2/zainmunirpatel/torch/install/share/luajit-2.1.0-beta1/HDF5.lua'
no file '/usr/local/share/lua/5.1/HDF5.lua'
no file '/usr/local/share/lua/5.1/HDF5/init.lua'
no file '/home/hugheslab2/zainmunirpatel/.luarocks/lib/lua/5.1/HDF5.so'
no file '/home/hugheslab2/zainmunirpatel/torch/install/lib/lua/5.1/HDF5.so'
no file '/home/hugheslab2/zainmunirpatel/torch/install/lib/HDF5.so'
no file './HDF5.so'
no file '/usr/local/lib/lua/5.1/HDF5.so'
no file '/usr/local/lib/lua/5.1/loadall.so'
stack traceback:
[C]: in function 'error'
...ainmunirpatel/torch/install/share/lua/5.1/trepl/init.lua:389: in function 'require'
[string "_RESULT={require 'HDF5'}"]:1: in main chunk
[C]: in function 'xpcall'
...ainmunirpatel/torch/install/share/lua/5.1/trepl/init.lua:661: in function 'repl'
...atel/torch/install/lib/luarocks/rocks/trepl/scm-1/bin/th:204: in main chunk
[C]: at 0x00406460
[0.0105s]
th> require 'hdf5'
{
H5Z_FILTER_CONFIG_ENCODE_ENABLED : 1
H5F_ACC_RDWR : 1
_getTorchType : function: 0x41b2fd18
H5F_OBJ_FILE : 1
H5S_ALL : 0
H5F_OBJ_GROUP : 4
C : userdata: 0x403b21f0
H5P_DEFAULT : 0
_describeObject : function: 0x41dc5718
H5Z_FILTER_NBIT : 5
_debugMode : false
_getObjectType : function: 0x41dc56d8
H5F_OBJ_ALL : 31
_getObjectName : function: 0x41b2fd38
version :
{
1 : 1
2 : 8
3 : 12
}
H5Z_FILTER_SHUFFLE : 2
HDF5Group : {...}
open : function: 0x402b8c50
H5Z_FILTER_SZIP : 4
H5F_OBJ_ATTR : 16
H5Z_FILTER_FLETCHER32 : 3
H5F_OBJ_DATATYPE : 8
debugMode : function: 0x402b8bd0
H5F_ACC_EXCL : 4
H5Z_FILTER_NONE : 0
_testUtils :
{
deepAlmostEq : function: 0x402b8b90
withTmpDir : function: 0x402b8af0
}
_nativeTypeForTensorType : function: 0x41b2fcb0
H5F_ACC_TRUNC : 2
_config :
{
HDF5_INCLUDE_PATH : "/usr/include"
HDF5_LIBRARIES : "/usr/lib64/libhdf5.so;/usr/lib64/libsz.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so"
}
_loadObject : function: 0x402b8c30
DataSetOptions : {...}
HDF5DataSet : {...}
H5Z_FILTER_RESERVED : 256
_logger :
{
error : function: 0x41b86850
warn : function: 0x41b86850
debug : function: 0x41b86898
}
H5F_ACC_RDONLY : 0
_fletcher32Available : function: 0x41dc5738
H5Z_FILTER_CONFIG_DECODE_ENABLED : 2
ffi :
{
abi : function: builtin#202
copy : function: builtin#200
errno : function: builtin#198
typeinfo : function: builtin#193
alignof : function: builtin#196
cdef : function: builtin#189
C : userdata: 0x41b8b398
cast : function: builtin#191
load : function: builtin#205
offsetof : function: builtin#197
sizeof : function: builtin#195
string : function: builtin#199
metatype : function: builtin#203
new : function: builtin#190
arch : "x64"
os : "Linux"
gc : function: builtin#204
fill : function: builtin#201
istype : function: builtin#194
typeof : function: builtin#192
}
H5Z_FILTER_ERROR : -1
_outputTypeForTensorType : function: 0x41b8df30
H5Z_FILTER_MAX : 65535
h5t :
{
STD_B32LE : 50331728
IEEE_F32BE : 50331703
NATIVE_B16 : 50331694
NATIVE_HSIZE : 50331698
NO_CLASS : -1
NATIVE_UINT_FAST32 : 50331681
STD_B8LE : 50331724
STD_I64BE : 50331715
NATIVE_LONG : 50331662
NATIVE_DOUBLE : 50331691
TIME : 2
NATIVE_INT16 : 50331670
NATIVE_LLONG : 50331688
STD_I8BE : 50331709
STD_B64LE : 50331730
NATIVE_HSSIZE : 50331699
STD_B32BE : 50331729
INTEGER : 0
NATIVE_INT64 : 50331682
STD_I8LE : 50331708
STD_I32LE : 50331712
NATIVE_SCHAR : 50331656
NATIVE_INT_FAST16 : 50331674
NATIVE_INT : 50331660
BITFIELD : 4
NATIVE_UINT_LEAST16 : 50331673
NATIVE_INT_LEAST16 : 50331672
IEEE_F64LE : 50331704
NATIVE_INT_FAST64 : 50331686
NATIVE_UINT_FAST64 : 50331687
NATIVE_UINT_LEAST64 : 50331685
NATIVE_INT_LEAST64 : 50331684
ENUM : 8
NATIVE_UINT64 : 50331683
NATIVE_HBOOL : 50331701
NATIVE_ULONG : 50331663
NATIVE_INT_FAST32 : 50331680
NATIVE_HADDR : 50331697
NATIVE_UINT : 50331661
NCLASSES : 11
NATIVE_UINT_LEAST32 : 50331679
NATIVE_INT_LEAST32 : 50331678
STD_U64LE : 50331722
NATIVE_UINT32 : 50331677
NATIVE_SHORT : 50331658
NATIVE_INT32 : 50331676
VLEN : 9
ARRAY : 10
STD_U16LE : 50331718
STD_B16LE : 50331726
STD_I64LE : 50331714
NATIVE_UINT16 : 50331671
NATIVE_UINT_FAST8 : 50331669
STD_B16BE : 50331727
NATIVE_INT_FAST8 : 50331668
FLOAT : 1
REFERENCE : 7
STD_U32LE : 50331720
NATIVE_USHORT : 50331659
NATIVE_ULLONG : 50331689
NATIVE_INT8 : 50331664
IEEE_F32LE : 50331702
STD_U8BE : 50331717
NATIVE_INT_LEAST8 : 50331666
NATIVE_UINT8 : 50331665
NATIVE_B32 : 50331695
NATIVE_HERR : 50331700
NATIVE_OPAQUE : 50331736
NATIVE_LDOUBLE : 50331692
NATIVE_UINT_LEAST8 : 50331667
COMPOUND : 6
STD_REF_OBJ : 50331739
NATIVE_UINT_FAST16 : 50331675
NATIVE_B64 : 50331696
STD_U16BE : 50331719
STD_REF_DSETREG : 50331740
NATIVE_B8 : 50331693
STD_I32BE : 50331713
IEEE_F64BE : 50331705
NATIVE_FLOAT : 50331690
NATIVE_UCHAR : 50331657
STD_U32BE : 50331721
OPAQUE : 5
STD_B64BE : 50331731
STD_U8LE : 50331716
STD_I16BE : 50331711
STD_B8BE : 50331725
STRING : 3
STD_I16LE : 50331710
STD_U64BE : 50331723
}
HDF5File : {...}
H5Z_FILTER_SCALEOFFSET : 6
H5Z_FILTER_DEFLATE : 1
H5F_ACC_CREAT : 16
H5F_UNLIMITED : 18446744073709551615ULL
_deflateAvailable : function: 0x41dc5780
_inDebugMode : function: 0x402b8c10
H5F_OBJ_LOCAL : 32
H5S_SELECT_SET : 0
_datatypeName : function: 0x41541360
H5F_ACC_DEBUG : 8
H5F_OBJ_DATASET : 2
}

This made me think that I might have not installed https://github.com/davek44/torch-hdf5.git properly. I re-installed it but still get the same ENUM error when I run basset_train.lua. Here are my installation logs for installing torch-hdf5. Was wondering if it should like this for a successful install for torch-hdf5?

[zainmunirpatel@bc2 torch-hdf5]$ luarocks make
cmake -E make_directory build;
cd build;
cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="/home/hugheslab2/zainmunirpatel/torch/install/bin/.." -DCMAKE_INSTALL_PREFIX="/home/hugheslab2/zainmunirpatel/torch/install/lib/luarocks/rocks/hdf5/0-0";
make

-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found Torch7 in /home/hugheslab2/zainmunirpatel/torch/install
-- Found HDF5: /usr/lib64/libhdf5.so;/usr/lib64/libsz.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (Required is at least version "1.8")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hugheslab2/zainmunirpatel/Basset/src/torch-hdf5/build
cd build && make install
Install the project...
-- Install configuration: "Release"
-- Generating /home/hugheslab2/zainmunirpatel/torch/install/lib/luarocks/rocks/hdf5/0-0/lua/hdf5/config.lua
-- Installing: /home/hugheslab2/zainmunirpatel/torch/install/lib/luarocks/rocks/hdf5/0-0/lua/hdf5/ffi.lua
-- Installing: /home/hugheslab2/zainmunirpatel/torch/install/lib/luarocks/rocks/hdf5/0-0/lua/hdf5/dataset.lua
-- Installing: /home/hugheslab2/zainmunirpatel/torch/install/lib/luarocks/rocks/hdf5/0-0/lua/hdf5/group.lua
-- Installing: /home/hugheslab2/zainmunirpatel/torch/install/lib/luarocks/rocks/hdf5/0-0/lua/hdf5/testUtils.lua
-- Installing: /home/hugheslab2/zainmunirpatel/torch/install/lib/luarocks/rocks/hdf5/0-0/lua/hdf5/file.lua
-- Installing: /home/hugheslab2/zainmunirpatel/torch/install/lib/luarocks/rocks/hdf5/0-0/lua/hdf5/datasetOptions.lua
-- Installing: /home/hugheslab2/zainmunirpatel/torch/install/lib/luarocks/rocks/hdf5/0-0/lua/hdf5/init.lua
Updating manifest for /home/hugheslab2/zainmunirpatel/torch/install/lib/luarocks/rocks
hdf5 0-0 is now built and installed in /home/hugheslab2/zainmunirpatel/torch/install/ (license: BSD)

Thanks for the help and let me know if you think there is some other issue.

Best,
Zain

from basset.

The last thing that I can think of is that you also have deepmind’s version of torch-hdf5 installed just like Sam in #25. Maybe uninstall torch-hdf5 to make sure you have a clean slate before installing my version.

Otherwise, I’m not sure I’m going to be able to figure this one out. So, I prioritize Basset-like behavior in the Basenji package to give you a path forward.

from basset.

Hi, I have Basset-like behavior implemented in Basenji now. Check out https://github.com/calico/basenji/tree/master/manuscripts/basset

from basset.

Hi Dave,
Thanks a lot for implementing this. I really appreciate it! I will check it out.
Best,
Zain

from basset.

Hi Dave, Thanks a lot for implementing this. I really appreciate it! I will check it out. Best, Zain

Hi,I have the nearly the same problem with you,but I can't figure out what's going wrong.I reinstall the hdf5 1.8.18. But I still receive ENUM error. Any idea will be appreciated!

from basset.

Hi Dave, Thanks a lot for implementing this. I really appreciate it! I will check it out. Best, Zain

Hi,I have the nearly the same problem with you,but I can't figure out what's going wrong.I reinstall the hdf5 1.8.18. But I still receive ENUM error. Any idea will be appreciated!

The error comes from your .h5 file
Before running "seq_hdf5.py"
make sure your h5py version is correct.
RUN:
conda install -c conda-forge h5py==2.6.0
everything will be OK!
update：
the src files are different from which deposited in docker

from basset.