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AMP-USERS  June 2018

AMP-USERS June 2018

Subject:

some problems about installation of Amp

From:

SUBSCRIBE AMP-USERS Mingxia Zhou <[log in to unmask]>

Reply-To:

Amp Users List <[log in to unmask]>

Date:

Mon, 18 Jun 2018 11:50:31 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (1065 lines)

Hi everyone,

My name is mingxia, I am a new user for Amp. However, I had some errors when install the Amp. 

Follow the installation instruction online, I think I have set the environment successfully. The problem occurs in building fortran modules. And when  I run the tests, the nosetests failed. After typing f2py -c -m fmodules model.f90 descriptor/cutoffs.f90 descriptor/gaussian.f90 descriptor/zernike.f90 model/neuralnetwork.f90, the output message is shown as:

 
f2py -c -m fmodules model.f90 descriptor/cutoffs.f90 descriptor/gaussian.f90 descriptor/zernike.f90 model/neuralnetwork.f90
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "fmodules" sources
f2py options: []
f2py:> /tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c
creating /tmp/tmpsjmi4xnt/src.linux-x86_64-3.6
Reading fortran codes...
        Reading file 'model.f90' (format:fix)
Line #99 in model.f90:"      type:: image_forces"
        analyzeline: No name/args pattern found for line.
Line #104 in model.f90:"      type:: integer_one_d_array"
        analyzeline: No name/args pattern found for line.
Line #109 in model.f90:"      type:: embedded_real_one_one_d_array"
        analyzeline: No name/args pattern found for line.
Line #114 in model.f90:"      type:: embedded_real_one_two_d_array"
        analyzeline: No name/args pattern found for line.
Line #119 in model.f90:"      type:: embedded_integer_one_one_d_array"
        analyzeline: No name/args pattern found for line.
Line #124 in model.f90:"      type:: embedded_one_one_two_d_array"
        analyzeline: No name/args pattern found for line.
rmbadname1: Replacing "index" with "index_bn".
        Reading file 'descriptor/cutoffs.f90' (format:fix)
        Reading file 'descriptor/gaussian.f90' (format:free)
        Reading file 'descriptor/zernike.f90' (format:free)
        Reading file 'model/neuralnetwork.f90' (format:fix)
Line #17 in model/neuralnetwork.f90:"      type:: real_two_d_array"
        analyzeline: No name/args pattern found for line.
Line #22 in model/neuralnetwork.f90:"      type:: element_parameters"
        analyzeline: No name/args pattern found for line.
Line #29 in model/neuralnetwork.f90:"      type:: real_one_d_array"
        analyzeline: No name/args pattern found for line.
Post-processing...
        Block: fmodules
                        Block: check_version
                        Block: fingerprint_props
                        Block: model_props
                        Block: images_props
{}
In: :fmodules:model.f90:calculate_loss:calculate_energy
vars2fortran: No typespec for argument "image_no".
{}
In: :fmodules:model.f90:calculate_loss:calculate_forces
vars2fortran: No typespec for argument "image_no".
{}
In: :fmodules:model.f90:calculate_loss:calculate_denergy_dparameters
vars2fortran: No typespec for argument "image_no".
{}
In: :fmodules:model.f90:calculate_loss:calculate_numerical_denergy_dparameters
vars2fortran: No typespec for argument "image_no".
{}
In: :fmodules:model.f90:calculate_loss:calculate_dforces_dparameters
vars2fortran: No typespec for argument "image_no".
{}
In: :fmodules:model.f90:calculate_loss:calculate_numerical_dforces_dparameters
vars2fortran: No typespec for argument "image_no".
                        Block: calculate_loss
In: :fmodules:model.f90:calculate_loss
get_useparameters: no module neuralnetwork info used by calculate_loss
                                Block: unknown_type
In: :fmodules:model.f90:calculate_loss:unknown_type
get_useparameters: no module neuralnetwork info used by unknown_type
                                Block: unknown_type
In: :fmodules:model.f90:calculate_loss:unknown_type
get_useparameters: no module neuralnetwork info used by unknown_type
                                Block: unknown_type
In: :fmodules:model.f90:calculate_loss:unknown_type
get_useparameters: no module neuralnetwork info used by unknown_type
                                Block: unknown_type
In: :fmodules:model.f90:calculate_loss:unknown_type
get_useparameters: no module neuralnetwork info used by unknown_type
                                Block: unknown_type
In: :fmodules:model.f90:calculate_loss:unknown_type
get_useparameters: no module neuralnetwork info used by unknown_type
                                Block: unknown_type
In: :fmodules:model.f90:calculate_loss:unknown_type
get_useparameters: no module neuralnetwork info used by unknown_type
                        Block: deallocate_variables
In: :fmodules:model.f90:deallocate_variables
get_useparameters: no module neuralnetwork info used by deallocate_variables
                        Block: cutoffs
                                Block: cutoff_fxn
                                Block: cutoff_fxn_prime
                        Block: calculate_g2
                        Block: calculate_g4
                        Block: calculate_g2_prime
                        Block: calculate_g4_prime
                        Block: calculate_zernike_prime
                        Block: calculate_z
                        Block: calculate_z_prime
                        Block: calculate_q
                        Block: binomial
                        Block: neuralnetwork
                                Block: unknown_type
                                Block: unknown_type
                                Block: unknown_type
                                Block: calculate_image_energy
                                Block: calculate_atomic_energy
                                Block: calculate_force_
                                Block: calculate_force
                                Block: calculate_denergy_dparameters_
                                Block: calculate_datomicenergy_dparameters
                                Block: calculate_dforce_dparameters_
                                Block: calculate_dforce_dparameters
Post-processing (stage 2)...
        Block: fmodules
                Block: unknown_interface
                        Block: check_version
                        Block: fingerprint_props
                        Block: model_props
                        Block: images_props
                        Block: calculate_loss
                                Block: unknown_type
                                Block: unknown_type
                                Block: unknown_type
                                Block: unknown_type
                                Block: unknown_type
                                Block: unknown_type
                        Block: deallocate_variables
                        Block: cutoffs
                                Block: cutoff_fxn
                                Block: cutoff_fxn_prime
                        Block: calculate_g2
                        Block: calculate_g4
                        Block: calculate_g2_prime
                        Block: calculate_g4_prime
                        Block: calculate_zernike_prime
                        Block: calculate_z
                        Block: calculate_z_prime
                        Block: calculate_q
                        Block: binomial
                        Block: neuralnetwork
                                Block: unknown_type
                                Block: unknown_type
                                Block: unknown_type
                                Block: calculate_image_energy
                                Block: calculate_atomic_energy
                                Block: calculate_force_
                                Block: calculate_force
                                Block: calculate_denergy_dparameters_
                                Block: calculate_datomicenergy_dparameters
                                Block: calculate_dforce_dparameters_
                                Block: calculate_dforce_dparameters
Building modules...
        Building module "fmodules"...
                Constructing wrapper function "check_version"...
                  warning = check_version(version)
                Constructing wrapper function "calculate_loss"...
                  loss,dloss_dparameters,energyloss,forceloss,energy_maxresid,force_maxresid = calculate_loss(parameters,lossprime,[num_parameters])
                Constructing wrapper function "deallocate_variables"...
                  deallocate_variables()
                Constructing wrapper function "calculate_g2"...
                  ridge = calculate_g2(neighbornumbers,neighborpositions,g_number,g_eta,rc,cutofffn,ri,[p_gamma])
                Constructing wrapper function "calculate_g4"...
                  ridge = calculate_g4(neighbornumbers,neighborpositions,g_numbers,g_gamma,g_zeta,g_eta,rc,cutofffn,ri,[p_gamma])
                Constructing wrapper function "calculate_g2_prime"...
                  ridge = calculate_g2_prime(neighborindices,neighbornumbers,neighborpositions,g_number,g_eta,rc,cutofffn,i,ri,m,l,[p_gamma])
                Constructing wrapper function "calculate_g4_prime"...
                  ridge = calculate_g4_prime(neighborindices,neighbornumbers,neighborpositions,g_numbers,g_gamma,g_zeta,g_eta,rc,cutofffn,i,ri,m,l,[p_gamma])
                Constructing wrapper function "calculate_zernike_prime"...
                  norm_prime = calculate_zernike_prime(n,l,n_indices,numbers,rs,g_numbers,cutoff,indexx,home,p,q,factorial,cutofffn,[n_length,fac_length,p_gamma])
                Constructing wrapper function "calculate_z"...
                  output = calculate_z(n,l,m,x,y,z,factorial,[length])
                Constructing wrapper function "calculate_z_prime"...
                  output = calculate_z_prime(n,l,m,x,y,z,p,factorial,[length])
                Constructing wrapper function "calculate_q"...
                  output = calculate_q(nu,k,l,factorial,[length])
                Constructing wrapper function "binomial"...
                  output = binomial(n,k,factorial,[length])
                Constructing F90 module support for "fingerprint_props"...
                  Variables: num_fingerprints_of_elements raveled_fingerprints raveled_fingerprintprimes
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
                Constructing F90 module support for "model_props"...
                  Variables: mode_signal train_forces energy_coefficient force_coefficient overfit numericprime d
                Constructing F90 module support for "images_props"...
                  Variables: num_images num_elements elements_numbers num_images_atoms atomic_numbers num_neighbors raveled_neighborlists actual_energies actual_forces num_atoms atomic_positions
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
                Constructing F90 module support for "cutoffs"...
                Creating wrapper for Fortran function "cutoff_fxn"("cutoff_fxn")...
                        Constructing wrapper function "cutoffs.cutoff_fxn"...
                          cutoff_fxn = cutoff_fxn(r,rc,cutofffn,[p_gamma])
                Creating wrapper for Fortran function "cutoff_fxn_prime"("cutoff_fxn_prime")...
                        Constructing wrapper function "cutoffs.cutoff_fxn_prime"...
                          cutoff_fxn_prime = cutoff_fxn_prime(r,rc,cutofffn,[p_gamma])
                Constructing F90 module support for "neuralnetwork"...
                  Variables: min_fingerprints max_fingerprints no_layers_of_elements no_nodes_of_elements activation_signal
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
getarrdims:warning: assumed shape array, using 0 instead of ':'
Skipping type unknown_type
Skipping type unknown_type
Skipping type unknown_type
                Creating wrapper for Fortran function "calculate_image_energy"("calculate_image_energy")...
                        Constructing wrapper function "neuralnetwork.calculate_image_energy"...
                          calculate_image_energy = calculate_image_energy(inputs,parameters,[num_inputs,num_parameters])
                Creating wrapper for Fortran function "calculate_atomic_energy"("calculate_atomic_energy")...
                        Constructing wrapper function "neuralnetwork.calculate_atomic_energy"...
                          calculate_atomic_energy = calculate_atomic_energy(symbol,fingerprint,elements_numbers,parameters,[len_of_fingerprint,num_elements,num_parameters])
                Creating wrapper for Fortran function "calculate_force_"("calculate_force_")...
                        Constructing wrapper function "neuralnetwork.calculate_force_"...
                          calculate_force_ = calculate_force_(inputs,inputs_,parameters,[num_inputs,num_parameters])
                Creating wrapper for Fortran function "calculate_force"("calculate_force")...
                        Constructing wrapper function "neuralnetwork.calculate_force"...
                          calculate_force = calculate_force(symbol,fingerprint,fingerprintprime,elements_numbers,parameters,[len_of_fingerprint,num_elements,num_parameters])
                Creating wrapper for Fortran function "calculate_denergy_dparameters_"("calculate_denergy_dparameters_")...
                        Constructing wrapper function "neuralnetwork.calculate_denergy_dparameters_"...
                          calculate_denergy_dparameters_ = calculate_denergy_dparameters_(inputs,parameters,[num_inputs,num_parameters])
                Creating wrapper for Fortran function "calculate_datomicenergy_dparameters"("calculate_datomicenergy_dparameters")...
                        Constructing wrapper function "neuralnetwork.calculate_datomicenergy_dparameters"...
                          calculate_datomicenergy_dparameters = calculate_datomicenergy_dparameters(symbol,fingerprint,elements_numbers,parameters,[len_of_fingerprint,num_elements,num_parameters])
                Creating wrapper for Fortran function "calculate_dforce_dparameters_"("calculate_dforce_dparameters_")...
                        Constructing wrapper function "neuralnetwork.calculate_dforce_dparameters_"...
                          calculate_dforce_dparameters_ = calculate_dforce_dparameters_(inputs,inputs_,parameters,[num_inputs,num_parameters])
                Creating wrapper for Fortran function "calculate_dforce_dparameters"("calculate_dforce_dparameters")...
                        Constructing wrapper function "neuralnetwork.calculate_dforce_dparameters"...
                          calculate_dforce_dparameters = calculate_dforce_dparameters(symbol,fingerprint,fingerprintprime,elements_numbers,parameters,[len_of_fingerprint,num_elements,num_parameters])
        Wrote C/API module "fmodules" to file "/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c"
        Fortran 90 wrappers are saved to "/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90"
  adding '/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fortranobject.c' to sources.
  adding '/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6' to include_dirs.
copying /soft/pymatgen/180120/lib/python3.6/site-packages/numpy/f2py/src/fortranobject.c -> /tmp/tmpsjmi4xnt/src.linux-x86_64-3.6
copying /soft/pymatgen/180120/lib/python3.6/site-packages/numpy/f2py/src/fortranobject.h -> /tmp/tmpsjmi4xnt/src.linux-x86_64-3.6
  adding '/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90' to sources.
build_src: building npy-pkg config files
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'fmodules' extension
compiling C sources
C compiler: gcc -pthread -B /soft/pymatgen/180120/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

creating /tmp/tmpsjmi4xnt/tmp
creating /tmp/tmpsjmi4xnt/tmp/tmpsjmi4xnt
creating /tmp/tmpsjmi4xnt/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6
compile options: '-I/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6 -I/soft/pymatgen/180120/lib/python3.6/site-packages/numpy/core/include -I/soft/pymatgen/180120/include/python3.6m -c'
gcc: /tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c
In file included from /soft/pymatgen/180120/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /soft/pymatgen/180120/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /soft/pymatgen/180120/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fortranobject.h:13,
                 from /tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:19:
/soft/pymatgen/180120/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c: In function 'f2py_setup_fingerprint_props':
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:3891:45: warning: assignment from incompatible pointer type [enabled by default]
   f2py_fingerprint_props_def[i_f2py++].func = num_fingerprints_of_elements;
                                             ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:3892:45: warning: assignment from incompatible pointer type [enabled by default]
   f2py_fingerprint_props_def[i_f2py++].func = raveled_fingerprints;
                                             ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:3893:45: warning: assignment from incompatible pointer type [enabled by default]
   f2py_fingerprint_props_def[i_f2py++].func = raveled_fingerprintprimes;
                                             ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c: In function 'f2py_setup_images_props':
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:3947:40: warning: assignment from incompatible pointer type [enabled by default]
   f2py_images_props_def[i_f2py++].func = elements_numbers;
                                        ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:3948:40: warning: assignment from incompatible pointer type [enabled by default]
   f2py_images_props_def[i_f2py++].func = num_images_atoms;
                                        ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:3949:40: warning: assignment from incompatible pointer type [enabled by default]
   f2py_images_props_def[i_f2py++].func = atomic_numbers;
                                        ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:3950:40: warning: assignment from incompatible pointer type [enabled by default]
   f2py_images_props_def[i_f2py++].func = num_neighbors;
                                        ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:3951:40: warning: assignment from incompatible pointer type [enabled by default]
   f2py_images_props_def[i_f2py++].func = raveled_neighborlists;
                                        ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:3952:40: warning: assignment from incompatible pointer type [enabled by default]
   f2py_images_props_def[i_f2py++].func = actual_energies;
                                        ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:3953:40: warning: assignment from incompatible pointer type [enabled by default]
   f2py_images_props_def[i_f2py++].func = actual_forces;
                                        ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:3955:40: warning: assignment from incompatible pointer type [enabled by default]
   f2py_images_props_def[i_f2py++].func = atomic_positions;
                                        ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c: In function 'f2py_setup_neuralnetwork':
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:3999:41: warning: assignment from incompatible pointer type [enabled by default]
   f2py_neuralnetwork_def[i_f2py++].func = min_fingerprints;
                                         ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:4000:41: warning: assignment from incompatible pointer type [enabled by default]
   f2py_neuralnetwork_def[i_f2py++].func = max_fingerprints;
                                         ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:4001:41: warning: assignment from incompatible pointer type [enabled by default]
   f2py_neuralnetwork_def[i_f2py++].func = no_layers_of_elements;
                                         ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:4002:41: warning: assignment from incompatible pointer type [enabled by default]
   f2py_neuralnetwork_def[i_f2py++].func = no_nodes_of_elements;
                                         ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c: At top level:
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.c:147:12: warning: 'f2py_size' defined but not used [-Wunused-function]
 static int f2py_size(PyArrayObject* var, ...)
            ^
gcc: /tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fortranobject.c
In file included from /soft/pymatgen/180120/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /soft/pymatgen/180120/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /soft/pymatgen/180120/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fortranobject.h:13,
                 from /tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fortranobject.c:2:
/soft/pymatgen/180120/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fortranobject.c: In function 'format_def':
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fortranobject.c:138:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (size < sizeof(notalloc)) {
                  ^
compiling Fortran 90 module sources
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
creating /tmp/tmpsjmi4xnt/descriptor
creating /tmp/tmpsjmi4xnt/model
compile options: '-I/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6 -I/soft/pymatgen/180120/lib/python3.6/site-packages/numpy/core/include -I/soft/pymatgen/180120/include/python3.6m -c'
extra options: '-J/tmp/tmpsjmi4xnt/ -I/tmp/tmpsjmi4xnt/'
gfortran:f90: model.f90
model.f90:219.1:

    do j = 1, num_parameters
 1
Warning: Nonconforming tab character at (1)
model.f90:220.1:

     denergy_dparameters(j) = 0.0d0
 1
Warning: Nonconforming tab character at (1)
model.f90:221.1:

    end do
 1
Warning: Nonconforming tab character at (1)
model.f90:269.1:

    do selfindex = 1, num_atoms
 1
Warning: Nonconforming tab character at (1)
model.f90:270.1:

     allocate(dforces_dparameters(&
 1
Warning: Nonconforming tab character at (1)
model.f90:271.1:

     selfindex)%twodarray(3, num_parameters))
 1
Warning: Nonconforming tab character at (1)
model.f90:272.1:

     do i = 1, 3
 1
Warning: Nonconforming tab character at (1)
model.f90:273.1:

         do j = 1, num_parameters
 1
Warning: Nonconforming tab character at (1)
model.f90:274.1:

             dforces_dparameters(&
 1
Warning: Nonconforming tab character at (1)
model.f90:275.1:

             selfindex)%twodarray(i, j) = 0.0d0
 1
Warning: Nonconforming tab character at (1)
model.f90:276.1:

         end do
 1
Warning: Nonconforming tab character at (1)
model.f90:277.1:

     end do
 1
Warning: Nonconforming tab character at (1)
model.f90:278.1:

    end do
 1
Warning: Nonconforming tab character at (1)
model.f90:300.1:

    do p = 1, size(dforces_dparameters)
 1
Warning: Nonconforming tab character at (1)
model.f90:301.1:

     deallocate(dforces_dparameters(p)%twodarray)
 1
Warning: Nonconforming tab character at (1)
model.f90:302.1:

    end do
 1
Warning: Nonconforming tab character at (1)
model.f90:303.1:

    deallocate(dforces_dparameters)
 1
Warning: Nonconforming tab character at (1)
model.f90:323.1:

        doverfitloss_dparameters(j) = &
 1
Warning: Nonconforming tab character at (1)
model.f90:646.1:

    allocate(fplus(num_atoms, 3))
 1
Warning: Nonconforming tab character at (1)
model.f90:647.1:

    do selfindex = 1, num_atoms
 1
Warning: Nonconforming tab character at (1)
model.f90:648.1:

   do i = 1, 3
 1
Warning: Nonconforming tab character at (1)
model.f90:649.1:

    fplus(selfindex, i) = amp_forces(selfindex, i)
 1
Warning: Nonconforming tab character at (1)
model.f90:650.1:

   end do
 1
Warning: Nonconforming tab character at (1)
model.f90:651.1:

    end do
 1
Warning: Nonconforming tab character at (1)
model.f90:655.1:

    allocate(fminus(num_atoms, 3))
 1
Warning: Nonconforming tab character at (1)
model.f90:656.1:

    do selfindex = 1, num_atoms
 1
Warning: Nonconforming tab character at (1)
model.f90:657.1:

   do i = 1, 3
 1
Warning: Nonconforming tab character at (1)
model.f90:658.1:

    fminus(selfindex, i) = amp_forces(selfindex, i)
 1
Warning: Nonconforming tab character at (1)
model.f90:659.1:

   end do
 1
Warning: Nonconforming tab character at (1)
model.f90:660.1:

    end do
 1
Warning: Nonconforming tab character at (1)
gfortran:f90: descriptor/cutoffs.f90
gfortran:f90: model/neuralnetwork.f90
model/neuralnetwork.f90:1379.1:

     unraveled_dforce_dweights(layer)%twodarray(p, q) = &
 1
Warning: Nonconforming tab character at (1)
model/neuralnetwork.f90:1380.1:

     -1.0d0 * unraveled_dforce_dweights(layer)%twodarray(p, q)
 1
Warning: Nonconforming tab character at (1)
model/neuralnetwork.f90:1767.1:

   unraveled_dforce_dparameters(element)%slope = &
 1
Warning: Nonconforming tab character at (1)
model/neuralnetwork.f90:1768.1:

   -1.0d0 * unraveled_dforce_dparameters(element)%slope
 1
Warning: Nonconforming tab character at (1)
model/neuralnetwork.f90:1802.1:

           unraveled_dforce_dparameters(element)%weights(&
 1
Warning: Nonconforming tab character at (1)
compiling Fortran sources
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
compile options: '-I/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6 -I/soft/pymatgen/180120/lib/python3.6/site-packages/numpy/core/include -I/soft/pymatgen/180120/include/python3.6m -c'
extra options: '-J/tmp/tmpsjmi4xnt/ -I/tmp/tmpsjmi4xnt/'
gfortran:f90: descriptor/gaussian.f90
gfortran:f90: descriptor/zernike.f90
gfortran:f90: /tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:102.10:

      use fingerprint_props, only : num_fingerprints_of_elements
          1
Warning: Unused module variable 'num_fingerprints_of_elements' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:102.10:

      use fingerprint_props, only : num_fingerprints_of_elements
          1
Warning: Unused module variable 'raveled_fingerprintprimes' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:102.10:

      use fingerprint_props, only : num_fingerprints_of_elements
          1
Warning: Unused module variable 'raveled_fingerprints' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:379.10:

      use images_props, only : num_images
          1
Warning: Unused module variable 'actual_energies' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:379.10:

      use images_props, only : num_images
          1
Warning: Unused module variable 'actual_forces' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:379.10:

      use images_props, only : num_images
          1
Warning: Unused module variable 'atomic_numbers' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:379.10:

      use images_props, only : num_images
          1
Warning: Unused module variable 'atomic_positions' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:379.10:

      use images_props, only : num_images
          1
Warning: Unused module variable 'elements_numbers' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:379.10:

      use images_props, only : num_images
          1
Warning: Unused module variable 'num_images_atoms' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:379.10:

      use images_props, only : num_images
          1
Warning: Unused module variable 'num_neighbors' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:379.10:

      use images_props, only : num_images
          1
Warning: Unused module variable 'raveled_neighborlists' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:706.10:

      use neuralnetwork, only : min_fingerprints
          1
Warning: Unused module variable 'max_fingerprints' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:706.10:

      use neuralnetwork, only : min_fingerprints
          1
Warning: Unused module variable 'min_fingerprints' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:706.10:

      use neuralnetwork, only : min_fingerprints
          1
Warning: Unused module variable 'no_layers_of_elements' which has been explicitly imported at (1)
/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.f90:706.10:

      use neuralnetwork, only : min_fingerprints
          1
Warning: Unused module variable 'no_nodes_of_elements' which has been explicitly imported at (1)
/usr/bin/gfortran -Wall -g -Wall -g -shared /tmp/tmpsjmi4xnt/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodulesmodule.o /tmp/tmpsjmi4xnt/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fortranobject.o /tmp/tmpsjmi4xnt/model.o /tmp/tmpsjmi4xnt/descriptor/cutoffs.o /tmp/tmpsjmi4xnt/model/neuralnetwork.o /tmp/tmpsjmi4xnt/descriptor/gaussian.o /tmp/tmpsjmi4xnt/descriptor/zernike.o /tmp/tmpsjmi4xnt/tmp/tmpsjmi4xnt/src.linux-x86_64-3.6/fmodules-f2pywrappers2.o -lgfortran -o ./fmodules.cpython-36m-x86_64-linux-gnu.so
Removing build directory /tmp/tmpsjmi4xnt




For the nosetests, the error message is shown as:


/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/__init__.py:27: UserWarning: Did not find fortran modules.
  warnings.warn('Did not find fortran modules.')
Gaussian/Neural non-periodic standard. ... ERROR
Gaussian/Neural periodic standard. ... ERROR
Gaussian/tflowNeural non-periodic. ... ok
Gaussian/tflowNeural periodic. ... ok
Gaussian/Neural training non-periodic standard test. ... ERROR
Gaussian/Neural training periodic standard test. ... ERROR
Guassian/Neural force call. ... ERROR
Guassian/Neural training. ... ERROR
Gaussian fingerprints consistency. ... ERROR
Zernike fingerprints consistency. ... ERROR
Displaced atom test. ... ok
FingerprintPlot test. ... ERROR
Gaussian/Neural numeric-analytic consistency. ... ERROR
Rotational/translational invariance. ... ok
/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/ase/lattice/surface.py:17: UserWarning: Moved to ase.build
  warnings.warn('Moved to ase.build')
Nodeplot creation test. ... ERROR
Gaussian/Neural train test. ... ERROR
Gaussian/tflow train test. ... ok

======================================================================
ERROR: Gaussian/Neural non-periodic standard.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/CuOPd_test/gaussian_neural_test/force_call_test.py", line 177, in non_periodic_test
    images]
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/CuOPd_test/gaussian_neural_test/force_call_test.py", line 176, in <listcomp>
    predicted_energies = [calc.get_potential_energy(image) for image in
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/ase/calculators/calculator.py", line 441, in get_potential_energy
    energy = self.get_property('energy', atoms)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/ase/calculators/calculator.py", line 486, in get_property
    self.calculate(atoms, [name], system_changes)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/__init__.py", line 254, in calculate
    calculate_derivatives=False)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 186, in calculate_fingerprints
    self.fingerprints.calculate_items(images, parallel=parallel, log=log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 440, in calculate_items
    d[key] = self.calc.calculate(images[key], key)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 303, in calculate
    index, symbol, neighborsymbols, neighborpositions)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 343, in get_fingerprint
    self.globals.cutoff, Ri, self.fortran)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 596, in calculate_G2
    ridge = fmodules.calculate_g2(**args_calculate_g2)
AttributeError: 'NoneType' object has no attribute 'calculate_g2'

======================================================================
ERROR: Gaussian/Neural periodic standard.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/CuOPd_test/gaussian_neural_test/force_call_test.py", line 322, in periodic_test
    images]
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/CuOPd_test/gaussian_neural_test/force_call_test.py", line 321, in <listcomp>
    predicted_energies = [calc.get_potential_energy(image) for image in
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/ase/calculators/calculator.py", line 441, in get_potential_energy
    energy = self.get_property('energy', atoms)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/ase/calculators/calculator.py", line 486, in get_property
    self.calculate(atoms, [name], system_changes)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/__init__.py", line 254, in calculate
    calculate_derivatives=False)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 186, in calculate_fingerprints
    self.fingerprints.calculate_items(images, parallel=parallel, log=log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 440, in calculate_items
    d[key] = self.calc.calculate(images[key], key)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 303, in calculate
    index, symbol, neighborsymbols, neighborpositions)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 343, in get_fingerprint
    self.globals.cutoff, Ri, self.fortran)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 596, in calculate_G2
    ridge = fmodules.calculate_g2(**args_calculate_g2)
AttributeError: 'NoneType' object has no attribute 'calculate_g2'

======================================================================
ERROR: Gaussian/Neural training non-periodic standard test.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/CuOPd_test/gaussian_neural_test/train_test.py", line 257, in non_periodic_0th_bfgs_step_test
    calc.train(images=images,)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/__init__.py", line 305, in train
    calculate_derivatives=train_forces)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 174, in calculate_fingerprints
    self.neighborlist.calculate_items(images, parallel=parallel, log=log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 446, in calculate_items
    sessions = setup_parallel(parallel, workercommand, log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 224, in setup_parallel
    parallel['envcommand']))
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 258, in start_workers
    child.expect('<amp-connect>')
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/spawnbase.py", line 315, in expect
    timeout, searchwindowsize, async)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/spawnbase.py", line 339, in expect_list
    return exp.expect_loop(timeout)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/expect.py", line 102, in expect_loop
    return self.eof(e)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/expect.py", line 49, in eof
    raise EOF(msg)
pexpect.exceptions.EOF: End Of File (EOF). Exception style platform.
<pexpect.pty_spawn.spawn object at 0x2b7ef1ed0f60>
command: /soft/gpaw/Anaconda3-4.2.0-171010/bin/python
args: ['/soft/gpaw/Anaconda3-4.2.0-171010/bin/python', '-m', 'amp.descriptor.gaussian', '0', 'beboplogin1:38404']
searcher: None
buffer (last 100 chars): b''
before (last 100 chars): b"ython: Error while finding spec for 'amp.descriptor.gaussian' (ImportError: No module named 'amp')\r\n"
after: <class 'pexpect.exceptions.EOF'>
match: None
match_index: None
exitstatus: None
flag_eof: True
pid: 106617
child_fd: 22
closed: False
timeout: 30
delimiter: <class 'pexpect.exceptions.EOF'>
logfile: None
logfile_read: None
logfile_send: None
maxread: 2000
ignorecase: False
searchwindowsize: None
delaybeforesend: 0.05
delayafterclose: 0.1
delayafterterminate: 0.1
-------------------- >> begin captured stdout << ---------------------
train-nonperiodic/False-1
diff at 204 = 2.7284841053187847e-12
train-nonperiodic/False-2

--------------------- >> end captured stdout << ----------------------

======================================================================
ERROR: Gaussian/Neural training periodic standard test.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/CuOPd_test/gaussian_neural_test/train_test.py", line 509, in periodic_0th_bfgs_step_test
    calc.train(images=images,)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/__init__.py", line 305, in train
    calculate_derivatives=train_forces)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 174, in calculate_fingerprints
    self.neighborlist.calculate_items(images, parallel=parallel, log=log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 446, in calculate_items
    sessions = setup_parallel(parallel, workercommand, log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 224, in setup_parallel
    parallel['envcommand']))
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 258, in start_workers
    child.expect('<amp-connect>')
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/spawnbase.py", line 315, in expect
    timeout, searchwindowsize, async)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/spawnbase.py", line 339, in expect_list
    return exp.expect_loop(timeout)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/expect.py", line 102, in expect_loop
    return self.eof(e)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/expect.py", line 49, in eof
    raise EOF(msg)
pexpect.exceptions.EOF: End Of File (EOF). Exception style platform.
<pexpect.pty_spawn.spawn object at 0x2b7ef1ed08d0>
command: /soft/gpaw/Anaconda3-4.2.0-171010/bin/python
args: ['/soft/gpaw/Anaconda3-4.2.0-171010/bin/python', '-m', 'amp.descriptor.gaussian', '0', 'beboplogin1:40236']
searcher: None
buffer (last 100 chars): b''
before (last 100 chars): b"ython: Error while finding spec for 'amp.descriptor.gaussian' (ImportError: No module named 'amp')\r\n"
after: <class 'pexpect.exceptions.EOF'>
match: None
match_index: None
exitstatus: None
flag_eof: True
pid: 106975
child_fd: 22
closed: False
timeout: 30
delimiter: <class 'pexpect.exceptions.EOF'>
logfile: None
logfile_read: None
logfile_send: None
maxread: 2000
ignorecase: False
searchwindowsize: None
delaybeforesend: 0.05
delayafterclose: 0.1
delayafterterminate: 0.1
-------------------- >> begin captured stdout << ---------------------
train-periodic/False-1
diff at 414 = 4.547473508864641e-12
train-periodic/False-2

--------------------- >> end captured stdout << ----------------------

======================================================================
ERROR: Guassian/Neural force call.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/consistency_test/gaussian_neural_test/force_call_test.py", line 530, in test
    for image in images]
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/consistency_test/gaussian_neural_test/force_call_test.py", line 530, in <listcomp>
    for image in images]
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/ase/calculators/calculator.py", line 441, in get_potential_energy
    energy = self.get_property('energy', atoms)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/ase/calculators/calculator.py", line 486, in get_property
    self.calculate(atoms, [name], system_changes)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/__init__.py", line 254, in calculate
    calculate_derivatives=False)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 186, in calculate_fingerprints
    self.fingerprints.calculate_items(images, parallel=parallel, log=log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 440, in calculate_items
    d[key] = self.calc.calculate(images[key], key)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 303, in calculate
    index, symbol, neighborsymbols, neighborpositions)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 343, in get_fingerprint
    self.globals.cutoff, Ri, self.fortran)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 596, in calculate_G2
    ridge = fmodules.calculate_g2(**args_calculate_g2)
AttributeError: 'NoneType' object has no attribute 'calculate_g2'

======================================================================
ERROR: Guassian/Neural training.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/consistency_test/gaussian_neural_test/train_test.py", line 566, in test
    calc.train(images=images,)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/__init__.py", line 311, in train
    parallel=self._parallel)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/model/neuralnetwork.py", line 228, in fit
    result = self.regressor.regress(model=self, log=log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/regression/__init__.py", line 85, in regress
    **self.optimizer_kwargs)
  File "/directory of the file//.local/lib/python3.5/site-packages/scipy/optimize/optimize.py", line 909, in fmin_bfgs
    res = _minimize_bfgs(f, x0, args, fprime, callback=callback, **opts)
  File "/directory of the file//.local/lib/python3.5/site-packages/scipy/optimize/optimize.py", line 963, in _minimize_bfgs
    gfk = myfprime(x0)
  File "/directory of the file//.local/lib/python3.5/site-packages/scipy/optimize/optimize.py", line 293, in function_wrapper
    return function(*(wrapper_args + args))
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/model/neuralnetwork.py", line 351, in get_lossprime
    lossprime=True)['dloss_dparameters']
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/model/__init__.py", line 570, in get_loss
    self._send_data_to_fortran()
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/model/__init__.py", line 534, in _send_data_to_fortran
    self.d)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/model/__init__.py", line 1061, in send_data_to_fortran
    _fmodules.images_props.num_images = num_images
AttributeError: 'NoneType' object has no attribute 'images_props'

======================================================================
ERROR: Gaussian fingerprints consistency.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/consistency_test/gaussian_test.py", line 89, in test
    calculate_derivatives=True)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 186, in calculate_fingerprints
    self.fingerprints.calculate_items(images, parallel=parallel, log=log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 440, in calculate_items
    d[key] = self.calc.calculate(images[key], key)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 303, in calculate
    index, symbol, neighborsymbols, neighborpositions)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 343, in get_fingerprint
    self.globals.cutoff, Ri, self.fortran)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 596, in calculate_G2
    ridge = fmodules.calculate_g2(**args_calculate_g2)
AttributeError: 'NoneType' object has no attribute 'calculate_g2'

======================================================================
ERROR: Zernike fingerprints consistency.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/consistency_test/zernike_test.py", line 55, in test
    calculate_derivatives=True)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/zernike.py", line 221, in calculate_fingerprints
    self.fingerprints.calculate_items(images, parallel=parallel, log=log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 440, in calculate_items
    d[key] = self.calc.calculate(images[key], key)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/zernike.py", line 331, in calculate
    indexfp = self.get_fingerprint(index, symbol, neighborsymbols, Rs)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/zernike.py", line 387, in get_fingerprint
    Z_nlm = fmodules.calculate_z(
AttributeError: 'NoneType' object has no attribute 'calculate_z'

======================================================================
ERROR: FingerprintPlot test.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/spawnbase.py", line 144, in read_nonblocking
    s = os.read(self.child_fd, size)
OSError: [Errno 5] Input/output error

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/expect.py", line 97, in expect_loop
    incoming = spawn.read_nonblocking(spawn.maxread, timeout)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/pty_spawn.py", line 455, in read_nonblocking
    return super(spawn, self).read_nonblocking(size)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/spawnbase.py", line 149, in read_nonblocking
    raise EOF('End Of File (EOF). Exception style platform.')
pexpect.exceptions.EOF: End Of File (EOF). Exception style platform.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/misc_test/fpplot_test.py", line 55, in test
    calc.train(images='fpplot-training.traj')
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/__init__.py", line 305, in train
    calculate_derivatives=train_forces)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 174, in calculate_fingerprints
    self.neighborlist.calculate_items(images, parallel=parallel, log=log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 446, in calculate_items
    sessions = setup_parallel(parallel, workercommand, log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 224, in setup_parallel
    parallel['envcommand']))
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 258, in start_workers
    child.expect('<amp-connect>')
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/spawnbase.py", line 315, in expect
    timeout, searchwindowsize, async)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/spawnbase.py", line 339, in expect_list
    return exp.expect_loop(timeout)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/expect.py", line 102, in expect_loop
    return self.eof(e)
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/pexpect/expect.py", line 49, in eof
    raise EOF(msg)
pexpect.exceptions.EOF: End Of File (EOF). Exception style platform.
<pexpect.pty_spawn.spawn object at 0x2b7efa67c470>
command: /soft/gpaw/Anaconda3-4.2.0-171010/bin/python
args: ['/soft/gpaw/Anaconda3-4.2.0-171010/bin/python', '-m', 'amp.descriptor.gaussian', '0', 'beboplogin1:38150']
searcher: None
buffer (last 100 chars): b''
before (last 100 chars): b"ython: Error while finding spec for 'amp.descriptor.gaussian' (ImportError: No module named 'amp')\r\n"
after: <class 'pexpect.exceptions.EOF'>
match: None
match_index: None
exitstatus: None
flag_eof: True
pid: 126251
child_fd: 21
closed: False
timeout: 30
delimiter: <class 'pexpect.exceptions.EOF'>
logfile: None
logfile_read: None
logfile_send: None
maxread: 2000
ignorecase: False
searchwindowsize: None
delaybeforesend: 0.05
delayafterclose: 0.1
delayafterterminate: 0.1

======================================================================
ERROR: Gaussian/Neural numeric-analytic consistency.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/misc_test/numeric_analytic_test.py", line 77, in test
    calc.train(images=images,)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/__init__.py", line 305, in train
    calculate_derivatives=train_forces)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 186, in calculate_fingerprints
    self.fingerprints.calculate_items(images, parallel=parallel, log=log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 440, in calculate_items
    d[key] = self.calc.calculate(images[key], key)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 303, in calculate
    index, symbol, neighborsymbols, neighborpositions)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 343, in get_fingerprint
    self.globals.cutoff, Ri, self.fortran)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 596, in calculate_G2
    ridge = fmodules.calculate_g2(**args_calculate_g2)
AttributeError: 'NoneType' object has no attribute 'calculate_g2'
-------------------- >> begin captured stdout << ---------------------
numeric_analytic_test/analytic-True-1

--------------------- >> end captured stdout << ----------------------

======================================================================
ERROR: Nodeplot creation test.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/test_NN_nodeplot.py", line 77, in test_nodeplot
    calc = train_data(images, setup_only=True)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/test_NN_nodeplot.py", line 65, in train_data
    calculate_derivatives=False)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 186, in calculate_fingerprints
    self.fingerprints.calculate_items(images, parallel=parallel, log=log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 440, in calculate_items
    d[key] = self.calc.calculate(images[key], key)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 303, in calculate
    index, symbol, neighborsymbols, neighborpositions)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 343, in get_fingerprint
    self.globals.cutoff, Ri, self.fortran)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 596, in calculate_G2
    ridge = fmodules.calculate_g2(**args_calculate_g2)
AttributeError: 'NoneType' object has no attribute 'calculate_g2'

======================================================================
ERROR: Gaussian/Neural train test.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/soft/gpaw/Anaconda3-4.2.0-171010/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/tests/test_gaussian_neural.py", line 56, in train_test
    calc.train(images=train_images,)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/__init__.py", line 305, in train
    calculate_derivatives=train_forces)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 186, in calculate_fingerprints
    self.fingerprints.calculate_items(images, parallel=parallel, log=log)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/utilities.py", line 440, in calculate_items
    d[key] = self.calc.calculate(images[key], key)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 303, in calculate
    index, symbol, neighborsymbols, neighborpositions)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 343, in get_fingerprint
    self.globals.cutoff, Ri, self.fortran)
  File "/directory of the file//soft/andrewpeterson-amp-a80158ba4871/amp/descriptor/gaussian.py", line 596, in calculate_G2
    ridge = fmodules.calculate_g2(**args_calculate_g2)
AttributeError: 'NoneType' object has no attribute 'calculate_g2'

----------------------------------------------------------------------
Ran 17 tests in 126.434s

FAILED (errors=12)



Do you know what's wrong during my installation process and how to solve it? Thank you for your patient and time. 

Thanks,
Mingxia

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