-- **************************************************************************
-- Starting configuration of Amber version 22.0.0...
-- CMake Version: 3.22.1
-- For how to use this build system, please read this wiki:
--     http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
-- For a list of important CMake variables, check here:
--     http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
-- **************************************************************************
-- Amber source found, building AmberTools and Amber
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) 
-- Downloading Python 3 Miniconda
-- Detected Linux OS. Downloading the Linux installer
-- Using 64 bit miniconda
-- Using cached Miniconda installer at /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/miniconda/download/Miniconda3-latest-Linux-x86_64.sh
Installing Miniconda Python.
PREFIX=/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/miniconda/install
Unpacking payload ...

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Extracting : conda-package-handling-1.9.0-py310h5eee18b_1.conda:   2%|▏         | 1/43 [00:00<00:05,  7.64it/s]
Extracting : tqdm-4.64.1-py310h06a4308_0.conda:   2%|▏         | 1/43 [00:00<00:05,  7.64it/s]                 
Extracting : pycparser-2.21-pyhd3eb1b0_0.conda:   5%|▍         | 2/43 [00:00<00:05,  7.64it/s]
Extracting : pycosat-0.6.4-py310h5eee18b_0.conda:   7%|▋         | 3/43 [00:00<00:05,  7.64it/s]
Extracting : pyopenssl-22.0.0-pyhd3eb1b0_0.conda:   9%|▉         | 4/43 [00:00<00:05,  7.64it/s]
Extracting : setuptools-65.5.0-py310h06a4308_0.conda:  12%|█▏        | 5/43 [00:00<00:04,  7.64it/s]
Extracting : _openmp_mutex-5.1-1_gnu.conda:  14%|█▍        | 6/43 [00:00<00:04,  7.64it/s]          
Extracting : ncurses-6.3-h5eee18b_3.conda:  16%|█▋        | 7/43 [00:00<00:04,  7.64it/s] 
Extracting : ncurses-6.3-h5eee18b_3.conda:  19%|█▊        | 8/43 [00:00<00:00, 38.18it/s]
Extracting : readline-8.2-h5eee18b_0.conda:  19%|█▊        | 8/43 [00:00<00:00, 38.18it/s]
Extracting : openssl-1.1.1s-h7f8727e_0.conda:  21%|██        | 9/43 [00:00<00:00, 38.18it/s]
Extracting : zlib-1.2.13-h5eee18b_0.conda:  23%|██▎       | 10/43 [00:00<00:00, 38.18it/s]  
Extracting : conda-22.11.1-py310h06a4308_4.conda:  26%|██▌       | 11/43 [00:00<00:00, 38.18it/s]
Extracting : _libgcc_mutex-0.1-main.conda:  28%|██▊       | 12/43 [00:00<00:00, 38.18it/s]       
Extracting : bzip2-1.0.8-h7b6447c_0.conda:  30%|███       | 13/43 [00:00<00:00, 38.18it/s]
Extracting : wheel-0.37.1-pyhd3eb1b0_0.conda:  33%|███▎      | 14/43 [00:00<00:00, 38.18it/s]
Extracting : pluggy-1.0.0-py310h06a4308_1.conda:  35%|███▍      | 15/43 [00:00<00:00, 38.18it/s]
Extracting : urllib3-1.26.13-py310h06a4308_0.conda:  37%|███▋      | 16/43 [00:00<00:00, 38.18it/s]
Extracting : libuuid-1.41.5-h5eee18b_0.conda:  40%|███▉      | 17/43 [00:00<00:00, 38.18it/s]      
Extracting : brotlipy-0.7.0-py310h7f8727e_1002.conda:  42%|████▏     | 18/43 [00:00<00:00, 38.18it/s]
Extracting : ruamel.yaml.clib-0.2.6-py310h5eee18b_1.conda:  44%|████▍     | 19/43 [00:00<00:00, 38.18it/s]
Extracting : pysocks-1.7.1-py310h06a4308_0.conda:  47%|████▋     | 20/43 [00:00<00:00, 38.18it/s]         
Extracting : pysocks-1.7.1-py310h06a4308_0.conda:  49%|████▉     | 21/43 [00:00<00:00, 73.60it/s]
Extracting : idna-3.4-py310h06a4308_0.conda:  49%|████▉     | 21/43 [00:00<00:00, 73.60it/s]     
Extracting : libgomp-11.2.0-h1234567_1.conda:  51%|█████     | 22/43 [00:00<00:00, 73.60it/s]
Extracting : xz-5.2.8-h5eee18b_0.conda:  53%|█████▎    | 23/43 [00:00<00:00, 73.60it/s]      
Extracting : tk-8.6.12-h1ccaba5_0.conda:  56%|█████▌    | 24/43 [00:00<00:00, 73.60it/s]
Extracting : requests-2.28.1-py310h06a4308_0.conda:  58%|█████▊    | 25/43 [00:00<00:00, 73.60it/s]
Extracting : cffi-1.15.1-py310h5eee18b_3.conda:  60%|██████    | 26/43 [00:00<00:00, 73.60it/s]    
Extracting : conda-content-trust-0.1.3-py310h06a4308_0.conda:  63%|██████▎   | 27/43 [00:00<00:00, 73.60it/s]
Extracting : libgcc-ng-11.2.0-h1234567_1.conda:  65%|██████▌   | 28/43 [00:00<00:00, 73.60it/s]              
Extracting : libgcc-ng-11.2.0-h1234567_1.conda:  67%|██████▋   | 29/43 [00:00<00:00, 54.90it/s]
Extracting : ruamel.yaml-0.17.21-py310h5eee18b_0.conda:  67%|██████▋   | 29/43 [00:00<00:00, 54.90it/s]
Extracting : python-3.10.8-h7a1cb2a_1.conda:  70%|██████▉   | 30/43 [00:00<00:00, 54.90it/s]           
Extracting : ca-certificates-2022.10.11-h06a4308_0.conda:  72%|███████▏  | 31/43 [00:00<00:00, 54.90it/s]
Extracting : libffi-3.4.2-h6a678d5_6.conda:  74%|███████▍  | 32/43 [00:00<00:00, 54.90it/s]              
Extracting : certifi-2022.12.7-py310h06a4308_0.conda:  77%|███████▋  | 33/43 [00:00<00:00, 54.90it/s]
Extracting : ld_impl_linux-64-2.38-h1181459_1.conda:  79%|███████▉  | 34/43 [00:00<00:00, 54.90it/s] 
Extracting : cryptography-38.0.1-py310h9ce1e76_0.conda:  81%|████████▏ | 35/43 [00:00<00:00, 54.90it/s]
Extracting : cryptography-38.0.1-py310h9ce1e76_0.conda:  84%|████████▎ | 36/43 [00:00<00:00, 52.96it/s]
Extracting : libstdcxx-ng-11.2.0-h1234567_1.conda:  84%|████████▎ | 36/43 [00:00<00:00, 52.96it/s]     
Extracting : toolz-0.12.0-py310h06a4308_0.conda:  86%|████████▌ | 37/43 [00:00<00:00, 52.96it/s]  
Extracting : pip-22.3.1-py310h06a4308_0.conda:  88%|████████▊ | 38/43 [00:00<00:00, 52.96it/s]  
Extracting : sqlite-3.40.0-h5082296_0.conda:  91%|█████████ | 39/43 [00:00<00:00, 52.96it/s]  
Extracting : six-1.16.0-pyhd3eb1b0_1.conda:  93%|█████████▎| 40/43 [00:00<00:00, 52.96it/s] 
Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda:  95%|█████████▌| 41/43 [00:00<00:00, 52.96it/s]
Extracting : tzdata-2022g-h04d1e81_0.conda:  98%|█████████▊| 42/43 [00:00<00:00, 52.96it/s]              
                                                                                           
Installing base environment...


Downloading and Extracting Packages


Downloading and Extracting Packages

Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
WARNING:
    You currently have a PYTHONPATH environment variable set. This may cause
    unexpected behavior when running the Python interpreter in Miniconda3.
    For best results, please verify that your PYTHONPATH only points to
    directories of packages that are compatible with the Python interpreter
    in Miniconda3: /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/miniconda/install
-- Updating and installing required and optional packages...
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

# All requested packages already installed.

Requirement already satisfied: pip in ./CMakeFiles/miniconda/install/lib/python3.10/site-packages (22.3.1)
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/miniconda/install

  added / updated specs:
    - nomkl


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    blas-1.0                   |         openblas          46 KB
    nomkl-3.0                  |                0          46 KB
    ------------------------------------------------------------
                                           Total:          91 KB

The following NEW packages will be INSTALLED:

  blas               pkgs/main/linux-64::blas-1.0-openblas 
  nomkl              pkgs/main/linux-64::nomkl-3.0-0 



Downloading and Extracting Packages

blas-1.0             | 46 KB     |            |   0% 

nomkl-3.0            | 46 KB     |            |   0% 

nomkl-3.0            | 46 KB     | ###5       |  35% 
blas-1.0             | 46 KB     | ###5       |  35% 

nomkl-3.0            | 46 KB     | ########## | 100% 

nomkl-3.0            | 46 KB     | ########## | 100% 
blas-1.0             | 46 KB     | ########## | 100% 
blas-1.0             | 46 KB     | ########## | 100% 
                                                     

                                                     
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/miniconda/install

  added / updated specs:
    - f90nml


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2022.12.7  |       ha878542_0         143 KB  conda-forge
    certifi-2022.12.7          |     pyhd8ed1ab_0         147 KB  conda-forge
    conda-22.11.1              |  py310hff52083_1         913 KB  conda-forge
    f90nml-1.4.3               |     pyhd8ed1ab_0          31 KB  conda-forge
    python_abi-3.10            |          2_cp310           4 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         1.2 MB

The following NEW packages will be INSTALLED:

  f90nml             conda-forge/noarch::f90nml-1.4.3-pyhd8ed1ab_0 
  python_abi         conda-forge/linux-64::python_abi-3.10-2_cp310 

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2022.10.11~ --> conda-forge::ca-certificates-2022.12.7-ha878542_0 

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi            pkgs/main/linux-64::certifi-2022.12.7~ --> conda-forge/noarch::certifi-2022.12.7-pyhd8ed1ab_0 
  conda              pkgs/main::conda-22.11.1-py310h06a430~ --> conda-forge::conda-22.11.1-py310hff52083_1 



Downloading and Extracting Packages

certifi-2022.12.7    | 147 KB    |            |   0% 

python_abi-3.10      | 4 KB      |            |   0% 


ca-certificates-2022 | 143 KB    |            |   0% 



f90nml-1.4.3         | 31 KB     |            |   0% 




conda-22.11.1        | 913 KB    |            |   0% 

python_abi-3.10      | 4 KB      | ########## | 100% 

python_abi-3.10      | 4 KB      | ########## | 100% 


ca-certificates-2022 | 143 KB    | #1         |  11% 
certifi-2022.12.7    | 147 KB    | #          |  11% 




conda-22.11.1        | 913 KB    | 1          |   2% 



f90nml-1.4.3         | 31 KB     | #####1     |  51% 




conda-22.11.1        | 913 KB    | ###1       |  32% 
certifi-2022.12.7    | 147 KB    | ########## | 100% 
certifi-2022.12.7    | 147 KB    | ########## | 100% 


ca-certificates-2022 | 143 KB    | ########## | 100% 


ca-certificates-2022 | 143 KB    | ########## | 100% 



f90nml-1.4.3         | 31 KB     | ########## | 100% 



f90nml-1.4.3         | 31 KB     | ########## | 100% 




conda-22.11.1        | 913 KB    | ########## | 100% 




conda-22.11.1        | 913 KB    | ########## | 100% 
                                                     

                                                     


                                                     



                                                     




                                                     
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/miniconda/install

  added / updated specs:
    - pandas


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bottleneck-1.3.5           |  py310ha9d4c09_0         274 KB
    libgfortran-ng-11.2.0      |       h00389a5_1          20 KB
    libgfortran5-11.2.0        |       h1234567_1         2.0 MB
    libopenblas-0.3.21         |       h043d6bf_0         5.4 MB
    numexpr-2.8.4              |  py310h757a811_0         134 KB
    numpy-1.23.4               |  py310hac523dd_0          10 KB
    numpy-base-1.23.4          |  py310h375b286_0         6.7 MB
    packaging-22.0             |  py310h06a4308_0          69 KB
    pandas-1.5.2               |  py310h1128e8f_0        11.9 MB
    python-dateutil-2.8.2      |     pyhd3eb1b0_0         233 KB
    pytz-2022.7                |  py310h06a4308_0         208 KB
    ------------------------------------------------------------
                                           Total:        27.0 MB

The following NEW packages will be INSTALLED:

  bottleneck         pkgs/main/linux-64::bottleneck-1.3.5-py310ha9d4c09_0 
  libgfortran-ng     pkgs/main/linux-64::libgfortran-ng-11.2.0-h00389a5_1 
  libgfortran5       pkgs/main/linux-64::libgfortran5-11.2.0-h1234567_1 
  libopenblas        pkgs/main/linux-64::libopenblas-0.3.21-h043d6bf_0 
  numexpr            pkgs/main/linux-64::numexpr-2.8.4-py310h757a811_0 
  numpy              pkgs/main/linux-64::numpy-1.23.4-py310hac523dd_0 
  numpy-base         pkgs/main/linux-64::numpy-base-1.23.4-py310h375b286_0 
  packaging          pkgs/main/linux-64::packaging-22.0-py310h06a4308_0 
  pandas             pkgs/main/linux-64::pandas-1.5.2-py310h1128e8f_0 
  python-dateutil    pkgs/main/noarch::python-dateutil-2.8.2-pyhd3eb1b0_0 
  pytz               pkgs/main/linux-64::pytz-2022.7-py310h06a4308_0 

The following packages will be UPDATED:

  conda              conda-forge::conda-22.11.1-py310hff52~ --> pkgs/main::conda-22.11.1-py310h06a4308_4 

The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2022.10.11-h06a4308_0 
  certifi            conda-forge/noarch::certifi-2022.12.7~ --> pkgs/main/linux-64::certifi-2022.12.7-py310h06a4308_0 



Downloading and Extracting Packages

packaging-22.0       | 69 KB     |            |   0% 

pytz-2022.7          | 208 KB    |            |   0% 


python-dateutil-2.8. | 233 KB    |            |   0% 



bottleneck-1.3.5     | 274 KB    |            |   0% 




libgfortran5-11.2.0  | 2.0 MB    |            |   0% 





numpy-base-1.23.4    | 6.7 MB    |            |   0% 






numexpr-2.8.4        | 134 KB    |            |   0% 







pandas-1.5.2         | 11.9 MB   |            |   0% 








libgfortran-ng-11.2. | 20 KB     |            |   0% 









numpy-1.23.4         | 10 KB     |            |   0% 










libopenblas-0.3.21   | 5.4 MB    |            |   0% 




libgfortran5-11.2.0  | 2.0 MB    |            |   1% 


python-dateutil-2.8. | 233 KB    | 6          |   7% 

pytz-2022.7          | 208 KB    | 7          |   8% 



bottleneck-1.3.5     | 274 KB    | 5          |   6% 
packaging-22.0       | 69 KB     | ##3        |  23% 




libgfortran5-11.2.0  | 2.0 MB    | #          |  11% 



bottleneck-1.3.5     | 274 KB    | ########7  |  88% 


python-dateutil-2.8. | 233 KB    | #########6 |  96% 





numpy-base-1.23.4    | 6.7 MB    |            |   0% 






numexpr-2.8.4        | 134 KB    | #1         |  12% 
packaging-22.0       | 69 KB     | ########## | 100% 
packaging-22.0       | 69 KB     | ########## | 100% 




libgfortran5-11.2.0  | 2.0 MB    | ###3       |  33% 








libgfortran-ng-11.2. | 20 KB     | ########1  |  81% 







pandas-1.5.2         | 11.9 MB   |            |   0% 





numpy-base-1.23.4    | 6.7 MB    | 2          |   3% 









numpy-1.23.4         | 10 KB     | ########## | 100% 







pandas-1.5.2         | 11.9 MB   | 2          |   3% 





numpy-base-1.23.4    | 6.7 MB    | 4          |   5% 










libopenblas-0.3.21   | 5.4 MB    |            |   0% 




libgfortran5-11.2.0  | 2.0 MB    | #######4   |  74% 

pytz-2022.7          | 208 KB    | ########## | 100% 

pytz-2022.7          | 208 KB    | ########## | 100% 







pandas-1.5.2         | 11.9 MB   | 4          |   4% 










libopenblas-0.3.21   | 5.4 MB    | #3         |  13% 





numpy-base-1.23.4    | 6.7 MB    | 6          |   7% 


python-dateutil-2.8. | 233 KB    | ########## | 100% 







pandas-1.5.2         | 11.9 MB   | 6          |   7% 










libopenblas-0.3.21   | 5.4 MB    | ##3        |  24% 





numpy-base-1.23.4    | 6.7 MB    | 9          |  10% 










libopenblas-0.3.21   | 5.4 MB    | ###8       |  38% 







pandas-1.5.2         | 11.9 MB   | 8          |   9% 





numpy-base-1.23.4    | 6.7 MB    | #1         |  12% 



bottleneck-1.3.5     | 274 KB    | ########## | 100% 










libopenblas-0.3.21   | 5.4 MB    | #####6     |  56% 







pandas-1.5.2         | 11.9 MB   | #1         |  11% 





numpy-base-1.23.4    | 6.7 MB    | #4         |  14% 






numexpr-2.8.4        | 134 KB    | ########## | 100% 






numexpr-2.8.4        | 134 KB    | ########## | 100% 










libopenblas-0.3.21   | 5.4 MB    | ######9    |  70% 







pandas-1.5.2         | 11.9 MB   | #3         |  13% 





numpy-base-1.23.4    | 6.7 MB    | #6         |  16% 








libgfortran-ng-11.2. | 20 KB     | ########## | 100% 










libopenblas-0.3.21   | 5.4 MB    | ########5  |  85% 







pandas-1.5.2         | 11.9 MB   | #5         |  15% 





numpy-base-1.23.4    | 6.7 MB    | #8         |  18% 







pandas-1.5.2         | 11.9 MB   | ##         |  20% 









numpy-1.23.4         | 10 KB     | ########## | 100% 





numpy-base-1.23.4    | 6.7 MB    | ##1        |  21% 







pandas-1.5.2         | 11.9 MB   | ##3        |  23% 




libgfortran5-11.2.0  | 2.0 MB    | ########## | 100% 




libgfortran5-11.2.0  | 2.0 MB    | ########## | 100% 










libopenblas-0.3.21   | 5.4 MB    | ########## | 100% 










libopenblas-0.3.21   | 5.4 MB    | ########## | 100% 





numpy-base-1.23.4    | 6.7 MB    | ##3        |  23% 







pandas-1.5.2         | 11.9 MB   | ##8        |  29% 





numpy-base-1.23.4    | 6.7 MB    | ##7        |  27% 







pandas-1.5.2         | 11.9 MB   | ####       |  40% 







pandas-1.5.2         | 11.9 MB   | ####5      |  45% 





numpy-base-1.23.4    | 6.7 MB    | ##9        |  29% 







pandas-1.5.2         | 11.9 MB   | #####6     |  56% 





numpy-base-1.23.4    | 6.7 MB    | ###3       |  34% 







pandas-1.5.2         | 11.9 MB   | ######2    |  62% 





numpy-base-1.23.4    | 6.7 MB    | ###6       |  37% 







pandas-1.5.2         | 11.9 MB   | ######8    |  69% 





numpy-base-1.23.4    | 6.7 MB    | ###9       |  40% 







pandas-1.5.2         | 11.9 MB   | #######9   |  80% 





numpy-base-1.23.4    | 6.7 MB    | ####3      |  44% 







pandas-1.5.2         | 11.9 MB   | ########6  |  86% 





numpy-base-1.23.4    | 6.7 MB    | ####7      |  47% 







pandas-1.5.2         | 11.9 MB   | #########6 |  96% 





numpy-base-1.23.4    | 6.7 MB    | #####1     |  51% 





numpy-base-1.23.4    | 6.7 MB    | #####4     |  55% 







pandas-1.5.2         | 11.9 MB   | ########## | 100% 





numpy-base-1.23.4    | 6.7 MB    | ######4    |  64% 





numpy-base-1.23.4    | 6.7 MB    | ######8    |  69% 





numpy-base-1.23.4    | 6.7 MB    | #######3   |  73% 





numpy-base-1.23.4    | 6.7 MB    | #######7   |  78% 





numpy-base-1.23.4    | 6.7 MB    | ########2  |  83% 





numpy-base-1.23.4    | 6.7 MB    | ########7  |  88% 





numpy-base-1.23.4    | 6.7 MB    | #########3 |  93% 





numpy-base-1.23.4    | 6.7 MB    | #########9 |  99% 





numpy-base-1.23.4    | 6.7 MB    | ########## | 100% 
                                                     

                                                     


                                                     



                                                     




                                                     





                                                     






                                                     







                                                     








                                                     









                                                     










                                                     
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/miniconda/install

  added / updated specs:
    - conda-build
    - cython=0.29
    - ipython
    - notebook
    - numpy
    - pytest
    - scipy


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    anyio-3.5.0                |  py310h06a4308_0         168 KB
    argon2-cffi-21.3.0         |     pyhd3eb1b0_0          15 KB
    argon2-cffi-bindings-21.2.0|  py310h7f8727e_0          72 KB
    asttokens-2.0.5            |     pyhd3eb1b0_0          20 KB
    attrs-22.1.0               |  py310h06a4308_0          86 KB
    backcall-0.2.0             |     pyhd3eb1b0_0          13 KB
    beautifulsoup4-4.11.1      |  py310h06a4308_0         188 KB
    bleach-4.1.0               |     pyhd3eb1b0_0         123 KB
    chardet-4.0.0              |py310h06a4308_1003         202 KB
    conda-build-3.23.3         |  py310h06a4308_0         580 KB
    cython-0.29.32             |  py310h6a678d5_0         4.3 MB
    debugpy-1.5.1              |  py310h295c915_0         1.7 MB
    decorator-5.1.1            |     pyhd3eb1b0_0          12 KB
    defusedxml-0.7.1           |     pyhd3eb1b0_0          23 KB
    entrypoints-0.4            |  py310h06a4308_0          16 KB
    executing-0.8.3            |     pyhd3eb1b0_0          18 KB
    fftw-3.3.9                 |       h27cfd23_1         2.3 MB
    filelock-3.6.0             |     pyhd3eb1b0_0          12 KB
    flit-core-3.6.0            |     pyhd3eb1b0_0          42 KB
    glob2-0.7                  |     pyhd3eb1b0_0          12 KB
    icu-58.2                   |       he6710b0_3        10.5 MB
    iniconfig-1.1.1            |     pyhd3eb1b0_0           8 KB
    ipykernel-6.15.2           |  py310h06a4308_0         192 KB
    ipython-8.7.0              |  py310h06a4308_0         1.0 MB
    ipython_genutils-0.2.0     |     pyhd3eb1b0_1          27 KB
    jedi-0.18.1                |  py310h06a4308_1         988 KB
    jinja2-2.11.3              |     pyhd3eb1b0_0         101 KB
    jsonschema-4.16.0          |  py310h06a4308_0         130 KB
    jupyter_client-7.4.8       |  py310h06a4308_0         207 KB
    jupyter_core-5.1.1         |  py310h06a4308_0          90 KB
    jupyter_server-1.23.4      |  py310h06a4308_0         385 KB
    jupyterlab_pygments-0.1.2  |             py_0           8 KB
    libarchive-3.6.1           |       hab531cd_0         815 KB
    liblief-0.12.3             |       h6a678d5_0         1.9 MB
    libsodium-1.0.18           |       h7b6447c_0         244 KB
    libxml2-2.9.14             |       h74e7548_0         718 KB
    lz4-c-1.9.4                |       h6a678d5_0         154 KB
    markupsafe-2.0.1           |  py310h7f8727e_0          35 KB
    matplotlib-inline-0.1.6    |  py310h06a4308_0          16 KB
    mistune-0.8.4              |py310h7f8727e_1000          55 KB
    nbclassic-0.4.8            |  py310h06a4308_0         5.8 MB
    nbclient-0.5.13            |  py310h06a4308_0          90 KB
    nbconvert-6.4.4            |  py310h06a4308_0         496 KB
    nbformat-5.7.0             |  py310h06a4308_0         134 KB
    nest-asyncio-1.5.5         |  py310h06a4308_0          16 KB
    notebook-6.5.2             |  py310h06a4308_0         514 KB
    notebook-shim-0.2.2        |  py310h06a4308_0          23 KB
    pandas-1.4.4               |  py310h6a678d5_0        25.5 MB
    pandocfilters-1.5.0        |     pyhd3eb1b0_0          11 KB
    parso-0.8.3                |     pyhd3eb1b0_0          70 KB
    patch-2.7.6                |    h7b6447c_1001         119 KB
    patchelf-0.15.0            |       h6a678d5_0          97 KB
    pexpect-4.8.0              |     pyhd3eb1b0_3          53 KB
    pickleshare-0.7.5          |  pyhd3eb1b0_1003          13 KB
    pkginfo-1.8.3              |  py310h06a4308_0          46 KB
    platformdirs-2.5.2         |  py310h06a4308_0          23 KB
    prometheus_client-0.14.1   |  py310h06a4308_0          91 KB
    prompt-toolkit-3.0.20      |     pyhd3eb1b0_0         259 KB
    psutil-5.9.0               |  py310h5eee18b_0         368 KB
    ptyprocess-0.7.0           |     pyhd3eb1b0_2          17 KB
    pure_eval-0.2.2            |     pyhd3eb1b0_0          14 KB
    py-1.11.0                  |     pyhd3eb1b0_0          76 KB
    py-lief-0.12.3             |  py310h6a678d5_0         1.4 MB
    pygments-2.11.2            |     pyhd3eb1b0_0         759 KB
    pyrsistent-0.18.0          |  py310h7f8727e_0         117 KB
    pytest-7.1.2               |  py310h06a4308_0         452 KB
    python-fastjsonschema-2.16.2|  py310h06a4308_0         231 KB
    python-libarchive-c-2.9    |     pyhd3eb1b0_1          47 KB
    pyyaml-6.0                 |  py310h5eee18b_1         178 KB
    pyzmq-23.2.0               |  py310h6a678d5_0        1017 KB
    ripgrep-13.0.0             |       hbdeaff8_0         1.1 MB
    scipy-1.9.3                |  py310heeff2f4_0        23.1 MB
    send2trash-1.8.0           |     pyhd3eb1b0_1          19 KB
    sniffio-1.2.0              |  py310h06a4308_1          15 KB
    soupsieve-2.3.2.post1      |  py310h06a4308_0          65 KB
    stack_data-0.2.0           |     pyhd3eb1b0_0          22 KB
    terminado-0.17.1           |  py310h06a4308_0          32 KB
    testpath-0.6.0             |  py310h06a4308_0          85 KB
    toml-0.10.2                |     pyhd3eb1b0_0          20 KB
    tomli-2.0.1                |  py310h06a4308_0          24 KB
    tornado-6.2                |  py310h5eee18b_0         602 KB
    traitlets-5.7.1            |  py310h06a4308_0         203 KB
    typing-extensions-4.4.0    |  py310h06a4308_0           8 KB
    typing_extensions-4.4.0    |  py310h06a4308_0          46 KB
    wcwidth-0.2.5              |     pyhd3eb1b0_0          26 KB
    webencodings-0.5.1         |  py310h06a4308_1          20 KB
    websocket-client-0.58.0    |  py310h06a4308_4          67 KB
    yaml-0.2.5                 |       h7b6447c_0          75 KB
    zeromq-4.3.4               |       h2531618_0         331 KB
    zstd-1.5.2                 |       ha4553b6_0         488 KB
    ------------------------------------------------------------
                                           Total:        91.7 MB

The following NEW packages will be INSTALLED:

  anyio              pkgs/main/linux-64::anyio-3.5.0-py310h06a4308_0 
  argon2-cffi        pkgs/main/noarch::argon2-cffi-21.3.0-pyhd3eb1b0_0 
  argon2-cffi-bindi~ pkgs/main/linux-64::argon2-cffi-bindings-21.2.0-py310h7f8727e_0 
  asttokens          pkgs/main/noarch::asttokens-2.0.5-pyhd3eb1b0_0 
  attrs              pkgs/main/linux-64::attrs-22.1.0-py310h06a4308_0 
  backcall           pkgs/main/noarch::backcall-0.2.0-pyhd3eb1b0_0 
  beautifulsoup4     pkgs/main/linux-64::beautifulsoup4-4.11.1-py310h06a4308_0 
  bleach             pkgs/main/noarch::bleach-4.1.0-pyhd3eb1b0_0 
  chardet            pkgs/main/linux-64::chardet-4.0.0-py310h06a4308_1003 
  conda-build        pkgs/main/linux-64::conda-build-3.23.3-py310h06a4308_0 
  cython             pkgs/main/linux-64::cython-0.29.32-py310h6a678d5_0 
  debugpy            pkgs/main/linux-64::debugpy-1.5.1-py310h295c915_0 
  decorator          pkgs/main/noarch::decorator-5.1.1-pyhd3eb1b0_0 
  defusedxml         pkgs/main/noarch::defusedxml-0.7.1-pyhd3eb1b0_0 
  entrypoints        pkgs/main/linux-64::entrypoints-0.4-py310h06a4308_0 
  executing          pkgs/main/noarch::executing-0.8.3-pyhd3eb1b0_0 
  fftw               pkgs/main/linux-64::fftw-3.3.9-h27cfd23_1 
  filelock           pkgs/main/noarch::filelock-3.6.0-pyhd3eb1b0_0 
  flit-core          pkgs/main/noarch::flit-core-3.6.0-pyhd3eb1b0_0 
  glob2              pkgs/main/noarch::glob2-0.7-pyhd3eb1b0_0 
  icu                pkgs/main/linux-64::icu-58.2-he6710b0_3 
  iniconfig          pkgs/main/noarch::iniconfig-1.1.1-pyhd3eb1b0_0 
  ipykernel          pkgs/main/linux-64::ipykernel-6.15.2-py310h06a4308_0 
  ipython            pkgs/main/linux-64::ipython-8.7.0-py310h06a4308_0 
  ipython_genutils   pkgs/main/noarch::ipython_genutils-0.2.0-pyhd3eb1b0_1 
  jedi               pkgs/main/linux-64::jedi-0.18.1-py310h06a4308_1 
  jinja2             pkgs/main/noarch::jinja2-2.11.3-pyhd3eb1b0_0 
  jsonschema         pkgs/main/linux-64::jsonschema-4.16.0-py310h06a4308_0 
  jupyter_client     pkgs/main/linux-64::jupyter_client-7.4.8-py310h06a4308_0 
  jupyter_core       pkgs/main/linux-64::jupyter_core-5.1.1-py310h06a4308_0 
  jupyter_server     pkgs/main/linux-64::jupyter_server-1.23.4-py310h06a4308_0 
  jupyterlab_pygmen~ pkgs/main/noarch::jupyterlab_pygments-0.1.2-py_0 
  libarchive         pkgs/main/linux-64::libarchive-3.6.1-hab531cd_0 
  liblief            pkgs/main/linux-64::liblief-0.12.3-h6a678d5_0 
  libsodium          pkgs/main/linux-64::libsodium-1.0.18-h7b6447c_0 
  libxml2            pkgs/main/linux-64::libxml2-2.9.14-h74e7548_0 
  lz4-c              pkgs/main/linux-64::lz4-c-1.9.4-h6a678d5_0 
  markupsafe         pkgs/main/linux-64::markupsafe-2.0.1-py310h7f8727e_0 
  matplotlib-inline  pkgs/main/linux-64::matplotlib-inline-0.1.6-py310h06a4308_0 
  mistune            pkgs/main/linux-64::mistune-0.8.4-py310h7f8727e_1000 
  nbclassic          pkgs/main/linux-64::nbclassic-0.4.8-py310h06a4308_0 
  nbclient           pkgs/main/linux-64::nbclient-0.5.13-py310h06a4308_0 
  nbconvert          pkgs/main/linux-64::nbconvert-6.4.4-py310h06a4308_0 
  nbformat           pkgs/main/linux-64::nbformat-5.7.0-py310h06a4308_0 
  nest-asyncio       pkgs/main/linux-64::nest-asyncio-1.5.5-py310h06a4308_0 
  notebook           pkgs/main/linux-64::notebook-6.5.2-py310h06a4308_0 
  notebook-shim      pkgs/main/linux-64::notebook-shim-0.2.2-py310h06a4308_0 
  pandocfilters      pkgs/main/noarch::pandocfilters-1.5.0-pyhd3eb1b0_0 
  parso              pkgs/main/noarch::parso-0.8.3-pyhd3eb1b0_0 
  patch              pkgs/main/linux-64::patch-2.7.6-h7b6447c_1001 
  patchelf           pkgs/main/linux-64::patchelf-0.15.0-h6a678d5_0 
  pexpect            pkgs/main/noarch::pexpect-4.8.0-pyhd3eb1b0_3 
  pickleshare        pkgs/main/noarch::pickleshare-0.7.5-pyhd3eb1b0_1003 
  pkginfo            pkgs/main/linux-64::pkginfo-1.8.3-py310h06a4308_0 
  platformdirs       pkgs/main/linux-64::platformdirs-2.5.2-py310h06a4308_0 
  prometheus_client  pkgs/main/linux-64::prometheus_client-0.14.1-py310h06a4308_0 
  prompt-toolkit     pkgs/main/noarch::prompt-toolkit-3.0.20-pyhd3eb1b0_0 
  psutil             pkgs/main/linux-64::psutil-5.9.0-py310h5eee18b_0 
  ptyprocess         pkgs/main/noarch::ptyprocess-0.7.0-pyhd3eb1b0_2 
  pure_eval          pkgs/main/noarch::pure_eval-0.2.2-pyhd3eb1b0_0 
  py                 pkgs/main/noarch::py-1.11.0-pyhd3eb1b0_0 
  py-lief            pkgs/main/linux-64::py-lief-0.12.3-py310h6a678d5_0 
  pygments           pkgs/main/noarch::pygments-2.11.2-pyhd3eb1b0_0 
  pyrsistent         pkgs/main/linux-64::pyrsistent-0.18.0-py310h7f8727e_0 
  pytest             pkgs/main/linux-64::pytest-7.1.2-py310h06a4308_0 
  python-fastjsonsc~ pkgs/main/linux-64::python-fastjsonschema-2.16.2-py310h06a4308_0 
  python-libarchive~ pkgs/main/noarch::python-libarchive-c-2.9-pyhd3eb1b0_1 
  pyyaml             pkgs/main/linux-64::pyyaml-6.0-py310h5eee18b_1 
  pyzmq              pkgs/main/linux-64::pyzmq-23.2.0-py310h6a678d5_0 
  ripgrep            pkgs/main/linux-64::ripgrep-13.0.0-hbdeaff8_0 
  scipy              pkgs/main/linux-64::scipy-1.9.3-py310heeff2f4_0 
  send2trash         pkgs/main/noarch::send2trash-1.8.0-pyhd3eb1b0_1 
  sniffio            pkgs/main/linux-64::sniffio-1.2.0-py310h06a4308_1 
  soupsieve          pkgs/main/linux-64::soupsieve-2.3.2.post1-py310h06a4308_0 
  stack_data         pkgs/main/noarch::stack_data-0.2.0-pyhd3eb1b0_0 
  terminado          pkgs/main/linux-64::terminado-0.17.1-py310h06a4308_0 
  testpath           pkgs/main/linux-64::testpath-0.6.0-py310h06a4308_0 
  toml               pkgs/main/noarch::toml-0.10.2-pyhd3eb1b0_0 
  tomli              pkgs/main/linux-64::tomli-2.0.1-py310h06a4308_0 
  tornado            pkgs/main/linux-64::tornado-6.2-py310h5eee18b_0 
  traitlets          pkgs/main/linux-64::traitlets-5.7.1-py310h06a4308_0 
  typing-extensions  pkgs/main/linux-64::typing-extensions-4.4.0-py310h06a4308_0 
  typing_extensions  pkgs/main/linux-64::typing_extensions-4.4.0-py310h06a4308_0 
  wcwidth            pkgs/main/noarch::wcwidth-0.2.5-pyhd3eb1b0_0 
  webencodings       pkgs/main/linux-64::webencodings-0.5.1-py310h06a4308_1 
  websocket-client   pkgs/main/linux-64::websocket-client-0.58.0-py310h06a4308_4 
  yaml               pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0 
  zeromq             pkgs/main/linux-64::zeromq-4.3.4-h2531618_0 
  zstd               pkgs/main/linux-64::zstd-1.5.2-ha4553b6_0 

The following packages will be DOWNGRADED:

  pandas                              1.5.2-py310h1128e8f_0 --> 1.4.4-py310h6a678d5_0 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting matplotlib
  Downloading matplotlib-3.6.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.8/11.8 MB 11.6 MB/s eta 0:00:00
Collecting cycler>=0.10
  Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Requirement already satisfied: python-dateutil>=2.7 in ./CMakeFiles/miniconda/install/lib/python3.10/site-packages (from matplotlib) (2.8.2)
Collecting pyparsing>=2.2.1
  Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 19.5 MB/s eta 0:00:00
Collecting fonttools>=4.22.0
  Downloading fonttools-4.38.0-py3-none-any.whl (965 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 965.4/965.4 kB 16.2 MB/s eta 0:00:00
Collecting pillow>=6.2.0
  Downloading Pillow-9.3.0-cp310-cp310-manylinux_2_28_x86_64.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 10.8 MB/s eta 0:00:00
Requirement already satisfied: packaging>=20.0 in ./CMakeFiles/miniconda/install/lib/python3.10/site-packages (from matplotlib) (22.0)
Collecting contourpy>=1.0.1
  Downloading contourpy-1.0.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (296 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 296.1/296.1 kB 21.4 MB/s eta 0:00:00
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.4.4-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 11.8 MB/s eta 0:00:00
Requirement already satisfied: numpy>=1.19 in ./CMakeFiles/miniconda/install/lib/python3.10/site-packages (from matplotlib) (1.23.4)
Requirement already satisfied: six>=1.5 in ./CMakeFiles/miniconda/install/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib) (1.16.0)
Installing collected packages: pyparsing, pillow, kiwisolver, fonttools, cycler, contourpy, matplotlib
Successfully installed contourpy-1.0.6 cycler-0.11.0 fonttools-4.38.0 kiwisolver-1.4.4 matplotlib-3.6.2 pillow-9.3.0 pyparsing-3.0.9
Will remove 151 (177.3 MB) tarball(s).
Will remove 1 index cache(s).
Will remove 12 (59.6 MB) package(s).
There are no tempfile(s) to remove.
There are no logfile(s) to remove.
-- Miniconda install successful!
-- Found PythonLibs: /home/rlwoltz/anaconda3/envs/AmberTools22/lib/libpython3.10.so (found version "3.10.8") 
-- Checking for Python package numpy -- found
-- Checking for Python package scipy -- found
-- Checking for Python package matplotlib -- found
-- Checking for Python package setuptools -- found
-- Checking for Python package tkinter -- found
-- Checking for Python package distutils.sysconfig -- found
-- Python relative site-packages location: <prefix>/lib/python3.10/site-packages
-- Looking for dlopen in dl
-- Looking for dlopen in dl - found
-- Found FLEX: /usr/bin/flex (found version "2.6.4") 
-- Found BISON: /usr/bin/bison (found version "3.8.2") 
-- Found X11: /home/rlwoltz/anaconda3/envs/AmberTools22/include   
-- Looking for XOpenDisplay in /home/rlwoltz/anaconda3/envs/AmberTools22/lib/libX11.so;/home/rlwoltz/anaconda3/envs/AmberTools22/lib/libXext.so
-- Looking for XOpenDisplay in /home/rlwoltz/anaconda3/envs/AmberTools22/lib/libX11.so;/home/rlwoltz/anaconda3/envs/AmberTools22/lib/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found Perl: /home/rlwoltz/anaconda3/envs/AmberTools22/bin/perl (found version "5.32.1") 
-- Found perl make: /usr/bin/make
-- Perl modules well be installed to AMBERHOME/lib/perl
-- Running updater... 
-- >>> Preparing to apply updates... please wait. 
-- >>> No new updates available for AmberTools 22 
-- >>> No new updates available for Amber 22 
-- Updater done.  If you want to install updates, then set the APPLY_UPDATES variable to true. 
-- Checking whether to use built-in libraries...
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Looking for complex.h
-- Looking for complex.h - found
-- Looking for rl_initialize in libreadline.so
-- Looking for rl_initialize in libreadline.so - found
-- Found Readline: /home/rlwoltz/anaconda3/envs/AmberTools22/include  
-- Unable to locate MKL_HOME for your system.  To use MKL, set MKL_HOME to point to your MKL installation location.
CMake Warning (dev) at /usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args` (OpenMP_C)
  does not match the name of the calling package (OpenMPFixed).  This can
  lead to problems in calling code that expects `find_package` result
  variables (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args)
  cmake/hanjianwei/FindMKL.cmake:194 (find_package)
  cmake/3rdPartyTools.cmake:223 (find_package)
  CMakeLists.txt:205 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found OpenMP_C: -fopenmp (found version "4.5") 
CMake Warning (dev) at /usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args` (OpenMP_CXX)
  does not match the name of the calling package (OpenMPFixed).  This can
  lead to problems in calling code that expects `find_package` result
  variables (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args)
  cmake/hanjianwei/FindMKL.cmake:194 (find_package)
  cmake/3rdPartyTools.cmake:223 (find_package)
  CMakeLists.txt:205 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
CMake Warning (dev) at /usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args`
  (OpenMP_Fortran) does not match the name of the calling package
  (OpenMPFixed).  This can lead to problems in calling code that expects
  `find_package` result variables (e.g., `_FOUND`) to follow a certain
  pattern.
Call Stack (most recent call first):
  cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args)
  cmake/hanjianwei/FindMKL.cmake:194 (find_package)
  cmake/3rdPartyTools.cmake:223 (find_package)
  CMakeLists.txt:205 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found OpenMP_Fortran: -fopenmp (found version "4.5") 
-- Performing Test SUPPORTS_NO_AS_NEEDED
-- Performing Test SUPPORTS_NO_AS_NEEDED - Success
-- Performing Test CMath_LINKS_WITHOUT_M
-- Performing Test CMath_LINKS_WITHOUT_M - Failed
-- Performing Test CMath_LINKS_WITH_M
-- Performing Test CMath_LINKS_WITH_M - Success
-- Found CMath: /home/rlwoltz/anaconda3/envs/AmberTools22/x86_64-conda-linux-gnu/sysroot/usr/lib/libm.so  
-- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY MKL_WORKS MKL_FORTRAN_WORKS) 
-- hints given to look for KMMD in DIR: 
-- found KMMD?:   /home/rlwoltz/anaconda3/envs/AmberTools22/lib/libkmmd.so
-- found INCLUDES?: 
-- Found KMMD:   
-- Looking for fftw_execute in libfftw3.so
-- Looking for fftw_execute in libfftw3.so - found
-- Looking for fftw_cleanup in libfftw3.so
-- Looking for fftw_cleanup in libfftw3.so - found
-- Found FFTW: /home/rlwoltz/anaconda3/envs/AmberTools22/lib/libfftw3.so  
-- Looking for nc_strerror in netcdf
-- Looking for nc_strerror in netcdf - found
-- Performing Test NetCDF_F90_WORKS
-- Performed Test NetCDF_F90_WORKS - Success
-- Found NetCDF: 1  found components: F77 F90 
-- Could NOT find Protobuf (missing: Protobuf_LIBRARIES Protobuf_INCLUDE_DIR) 
-- Looking for BLAS_dgemm_x in libxblas-amb.a
-- Looking for BLAS_dgemm_x in libxblas-amb.a - found
-- Looking for BLAS_dgemm_x in libxblas-amb.a
-- Looking for BLAS_dgemm_x in libxblas-amb.a - found
-- Found XBLAS: /home/rlwoltz/anaconda3/envs/AmberTools22/lib/libxblas-amb.a  
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Looking for dsaupd in libarpack.so
-- Looking for dsaupd in libarpack.so - found
-- Looking for arsecond in libarpack.so
-- Looking for arsecond in libarpack.so - not found
-- Detailed information about why this check failed can be found in /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeError.log
-- Found ARPACK: /home/rlwoltz/anaconda3/envs/AmberTools22/lib/libarpack.so  
-- Could not find some or all of the five main APBS libraries. Please set APBS_GENERIC_LIB, APBS_ROUTINES_LIB, 
APBS_PMGC_LIB, APBS_MG_LIB, and APBS_MALOC_LIB to point to the correct libraries (missing: APBS_API_LIB APBS_ROUTINES_LIB APBS_MG_LIB APBS_PMGC_LIB APBS_GENERIC_LIB APBS_MALOC_LIB APBS_WORKS APBS_INCLUDES) 
-- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH) 
-- Could NOT find PUPIL (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB PUPIL_TIME_LIB JNI_FOUND PUPIL_WORKS) 
-- Could NOT find LIO (missing: LIO_G2G_LIBRARY LIO_AMBER_LIBRARY LIO_WORKS) 
-- Could NOT find PLUMED (missing: PLUMED_LIBRARY PLUMED_KERNEL_LIBRARY PLUMED_INCLUDES PLUMED_WORKS) (Required is at least version "2.5")
-- Found ZLIB: /home/rlwoltz/anaconda3/envs/AmberTools22/lib/libz.so (found version "1.2.13") 
-- Found BZip2: /home/rlwoltz/anaconda3/envs/AmberTools22/lib/libbz2.so (found version "1.0.8") 
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Checking for perl module Chemistry::Mol
-- Checking for perl module Chemistry::Mol - failed
-- Checking for perl module ExtUtils::MakeMaker
-- Checking for perl module ExtUtils::MakeMaker - found at /home/rlwoltz/anaconda3/envs/AmberTools22/lib/perl5/core_perl/ExtUtils/MakeMaker.pm
-- Failed to find Perl modules: Chemistry::Mol (missing: PERLMODULES_CHEMISTRY_MOL_MODULE) 
-- Found Boost: /home/rlwoltz/anaconda3/envs/AmberTools22/lib/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: thread system program_options iostreams regex timer chrono filesystem graph 
-- Looking for boost::system::system_error() in -lpthread libboost_thread.so.1.74.0 libboost_system.so.1.74.0 libboost_program_options.so.1.74.0 libboost_iostreams.so.1.74.0 libboost_regex.so.1.74.0 libboost_chrono.so.1.74.0 libboost_timer.so.1.74.0 libboost_chrono.so.1.74.0 libboost_filesystem.so.1.74.0 libboost_regex.so.1.74.0 libboost_graph.so.1.74.0
-- Looking for boost::system::system_error() in -lpthread libboost_thread.so.1.74.0 libboost_system.so.1.74.0 libboost_program_options.so.1.74.0 libboost_iostreams.so.1.74.0 libboost_regex.so.1.74.0 libboost_chrono.so.1.74.0 libboost_timer.so.1.74.0 libboost_chrono.so.1.74.0 libboost_filesystem.so.1.74.0 libboost_regex.so.1.74.0 libboost_graph.so.1.74.0 - found
-- Looking for boost::iostreams::bzip2_decompressor() and boost::iostreams::gzip_decompressor() in -lpthread libboost_thread.so.1.74.0 libboost_system.so.1.74.0 libboost_program_options.so.1.74.0 libboost_iostreams.so.1.74.0 libboost_regex.so.1.74.0 libboost_chrono.so.1.74.0 libboost_timer.so.1.74.0 libboost_chrono.so.1.74.0 libboost_filesystem.so.1.74.0 libboost_regex.so.1.74.0 libboost_graph.so.1.74.0
-- Looking for boost::iostreams::bzip2_decompressor() and boost::iostreams::gzip_decompressor() in -lpthread libboost_thread.so.1.74.0 libboost_system.so.1.74.0 libboost_program_options.so.1.74.0 libboost_iostreams.so.1.74.0 libboost_regex.so.1.74.0 libboost_chrono.so.1.74.0 libboost_timer.so.1.74.0 libboost_chrono.so.1.74.0 libboost_filesystem.so.1.74.0 libboost_regex.so.1.74.0 libboost_graph.so.1.74.0 - found
-- Could NOT find MBX (missing: MBX_DIR)
-- Could not find MBX.  To locate it, add its install dir to the prefix path.
-- Could NOT find tng_io (missing: tng_io_DIR)
-- Could not find tng_io.  To locate it, add its install dir to the prefix path.
-- The following libraries were found on your system, but are not being used: boost
-- This is because the Amber devs have frequently seen broken installs of these libraries causing trouble.
-- To tell Amber to link to these libraries, you can select individual ones using -DFORCE_EXTERNAL_LIBS=<names>.
-- Alternatively, you can request that Amber link to all libraries it finds using -DTRUST_SYSTEM_LIBS=TRUE.
-- System arpack is missing the arsecond_ function.  That function will be built inside amber
-- Cannot find PLUMED.  You will still be able to load it at runtime.  If you want to link it at build time, set PLUMED_ROOT to where you installed it.
-- Performing Test SUPPORTS_WNO_UNUSED_LOCAL_TYPEDEFS
-- Performing Test SUPPORTS_WNO_UNUSED_LOCAL_TYPEDEFS - Success
-- Looking for mkstemp
-- Looking for mkstemp - found
-- Generating amber source scripts
-- Configuring subdirs...
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Reticulating splines...
-- Looking for sscanf
-- Looking for sscanf - found
-- Looking for stat
-- Looking for stat - found
CMake Error at AmberTools/src/kmmd/CMakeLists.txt:15 (add_library):
  add_library cannot create target "kmmd" because another target with the
  same name already exists.  The existing target is an interface library
  created in source directory "/home/rlwoltz/protein_modeling/amber22_src".
  See documentation for policy CMP0002 for more details.


-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of long double
-- Check size of long double - done
-- Found C++11 support: cxx_std_11
-- Looking for getline
-- Looking for getline - found
-- Performing Test SUPPORTS_WNO_UNUSED_RESULT
-- Performing Test SUPPORTS_WNO_UNUSED_RESULT - Success
-- Looking for backtrace
-- Looking for backtrace - found
-- Looking for getopt.h
-- Looking for getopt.h - found
-- Looking for sys/param.h
-- Looking for sys/param.h - found
-- Looking for sys/dir.h
-- Looking for sys/dir.h - found
-- Looking for dirent.h
-- Looking for dirent.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for pwd.h
-- Looking for pwd.h - found
-- Looking for stdbool.h
-- Looking for stdbool.h - found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for Windows.h
-- Looking for Windows.h - not found
-- Looking for X11/Xmd.h
-- Looking for X11/Xmd.h - found
-- Looking for toupper
-- Looking for toupper - found
-- Looking for tolower
-- Looking for tolower - found
-- Check size of BOOL
-- Check size of BOOL - done
-- Check size of _Bool
-- Check size of _Bool - done
CMake Warning at src/pmemd/src/xray/CMakeLists.txt:25 (message):
  PMEMD_XRAY_CPU_FFT_BACKEND=NONE disables xray functionality of `pmemd`
  executable


-- KMMD_LIB: /home/rlwoltz/anaconda3/envs/AmberTools22/lib/libkmmd.so
If you can't see the following build report, then you need to turn off COLOR_CMAKE_MESSAGES
-- ************************************************************************** 
--                               Build Report 
--                              Compiler Flags: 
-- C No-Opt:          -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -fcommon -O0 
-- C Optimized:       -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -fcommon -O3 -mtune=native 
-- 
-- CXX No-Opt:        -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -O0 
-- CXX Optimized:     -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -O3 -mtune=native 
-- 
-- Fortran No-Opt:    -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -fallow-argument-mismatch -fno-inline-arg-packing -O0 
-- Fortran Optimized: -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -fallow-argument-mismatch -fno-inline-arg-packing -O3 -mtune=native 
-- 
--                           3rd Party Libraries 
-- ---building bundled: ----------------------------------------------------- 
-- boost - C++ support library 
-- tng_io - enables GROMACS tng trajectory input in cpptraj 
-- perlmol - chemistry library used by FEW 
-- ---using installed: ------------------------------------------------------ 
-- blas - for fundamental linear algebra calculations 
-- lapack - for fundamental linear algebra calculations 
-- arpack - for fundamental linear algebra calculations 
-- ucpp - used as a preprocessor for the NAB compiler 
-- netcdf - for creating trajectory data files 
-- netcdf-fortran - for creating trajectory data files from Fortran 
-- fftw - used to do Fourier transforms very quickly 
-- readline - enables an interactive terminal in cpptraj 
-- xblas - used for high-precision linear algebra calculations 
-- zlib - for various compression and decompression tasks 
-- libbz2 - for bzip2 compression in cpptraj 
-- libm - for fundamental math routines if they are not contained in the C library 
-- kmmd - Machine-learning molecular dynamics 
-- ---disabled: ------------------------------------------------ 
-- c9x-complex - used as a support library on systems that do not have C99 complex.h support 
-- protobuf - protocol buffers library, used for communication with external software in QM/MM 
-- lio - used by Sander to run certain QM routines on the GPU 
-- apbs - used by Sander as an alternate Poisson-Boltzmann equation solver 
-- pupil - used by Sander as an alternate user interface 
-- plumed - used as an alternate MD backend for Sander 
-- mkl - alternate implementation of lapack and blas that is tuned for speed 
-- mbx - computes energies and forces for pmemd with the MB-pol model 

--                                Features: 
-- MPI:                     OFF 
-- OpenMP:                  OFF 
-- CUDA:                    OFF 
-- Build Shared Libraries:  ON 
-- Build GUI Interfaces:    ON 
-- Build Python Programs:   ON 
--  -Python Interpreter:    Internal Miniconda (version 3.10) 
-- Build Perl Programs:     ON 
-- Build configuration:     RELEASE 
-- Target Processor:        x86_64 
-- Build Documentation:     OFF 
-- Sander Variants:         normal LES API LES-API 
-- Install location:        /home/rlwoltz/protein_modeling/amber22/ 
-- Installation of Tests:   ON 

--                               Compilers: 
--         C: GNU 11.3.0 (/home/rlwoltz/anaconda3/envs/AmberTools22/bin/gcc) 
--       CXX: GNU 11.3.0 (/home/rlwoltz/anaconda3/envs/AmberTools22/bin/g++) 
--   Fortran: GNU 11.3.0 (/home/rlwoltz/anaconda3/envs/AmberTools22/bin/gfortran) 

--                              Building Tools: 
-- addles amberlite ambpdb antechamber cifparse cphstats cpptraj emil etc few gbnsr6 gem.pmemd kmmd leap lib mdgx mm_pbsa mmpbsa_py moft nab ndiff-2.00 nfe-umbrella-slice nmode nmr_aux packmol_memgen paramfit parmed pbsa pdb4amber pmemd pymsmt pysander pytraj reduce rism sander saxs sebomd sff sqm xray xtalutil 

--                            NOT Building Tools: 
-- quick - BUILD_QUICK is not enabled 
-- tcpb-cpp - BUILD_TCPB is not enabled 
-- tcpb-cpp/pytcpb - BUILD_TCPB is not enabled 
-- reaxff_puremd - BUILD_REAXFF_PUREMD is not enabled 
-- gpu_utils - Requires CUDA 
-- ************************************************************************** 
-- Environment resource files are provided to set the proper environment
-- variables to use AMBER and AmberTools. This is required to run any Python
-- programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)
-- 
-- If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
-- /home/rlwoltz/protein_modeling/amber22//amber.sh file in your shell. Consider adding the line
--   test -f /home/rlwoltz/protein_modeling/amber22//amber.sh && source /home/rlwoltz/protein_modeling/amber22//amber.sh
-- to your startup file (e.g., ~/.bashrc)
-- 
-- If you use a C shell (e.g., csh, tcsh), source the
-- /home/rlwoltz/protein_modeling/amber22//amber.csh file in your shell. Consider adding the line
--   test -f /home/rlwoltz/protein_modeling/amber22//amber.csh && source /home/rlwoltz/protein_modeling/amber22//amber.csh
-- to your startup file (e.g., ~/.cshrc)
-- 
-- Amber will be installed to /home/rlwoltz/protein_modeling/amber22/
-- Configuring incomplete, errors occurred!
See also "/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeOutput.log".
See also "/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeError.log".