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Further work to support ESMFold mining #16

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1 change: 1 addition & 0 deletions go.sum
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Original file line number Diff line number Diff line change
Expand Up @@ -1243,6 +1243,7 @@ golang.org/x/time v0.0.0-20181108054448-85acf8d2951c/go.mod h1:tRJNPiyCQ0inRvYxb
golang.org/x/time v0.0.0-20190308202827-9d24e82272b4/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ=
golang.org/x/time v0.3.0 h1:rg5rLMjNzMS1RkNLzCG38eapWhnYLFYXDXj2gOlr8j4=
golang.org/x/time v0.3.0/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ=
golang.org/x/time v0.6.0 h1:eTDhh4ZXt5Qf0augr54TN6suAUudPcawVZeIAPU7D4U=
golang.org/x/tools v0.0.0-20180221164845-07fd8470d635/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
golang.org/x/tools v0.0.0-20180828015842-6cd1fcedba52/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
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187 changes: 110 additions & 77 deletions models/esmfold.go
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Original file line number Diff line number Diff line change
Expand Up @@ -10,19 +10,25 @@ import (
"gobius/config"
"gobius/ipfs"
"gobius/utils"
"io"
"net/http"
"path/filepath"
"strings"
"time"

"os"
"os/exec"
"crypto/tls"

"github.com/google/uuid"
"github.com/mr-tron/base58"
"github.com/rs/zerolog"
)

type ESMFoldV1Input struct {
Sequence string `json:"sequence"`
type ESMFoldV1Inner struct {
Prompt string `json:"prompt"`
}

type ESMFoldV1Prompt struct {
Input ESMFoldV1Inner `json:"input"`
}

type ESMFoldV1Model struct {
Expand Down Expand Up @@ -51,7 +57,7 @@ var ESMFoldV1ModelTemplate = Model{
"version": 1,
"input": []map[string]any{
{
"variable": "sequence",
"variable": "prompt",
"type": "string",
"required": true,
"default": "",
Expand Down Expand Up @@ -79,40 +85,46 @@ func NewESMFoldV1Model(client ipfs.IPFSClient, appConfig *config.AppConfig, logg
return nil
}

http := &http.Client{
Transport: &http.Transport{MaxIdleConnsPerHost: 10},
}
httpClient := &http.Client{
Transport: &http.Transport{
MaxIdleConnsPerHost: 10,
ForceAttemptHTTP2: true,
TLSClientConfig: &tls.Config{InsecureSkipVerify: true},
},
CheckRedirect: func(req *http.Request, via []*http.Request) error {
if len(via) >= 10 {
return fmt.Errorf("too many redirects")
}
logger.Debug().Str("redirect_url", req.URL.String()).Msg("Following redirect")
return nil
},
Timeout: 600 * time.Second,
}

timeout := 600 * time.Second
ipfsTimeout := 30 * time.Second

// Use model.ID (the hex string CID) as the key for the Cog map
cogConfig, ok := appConfig.ML.Cog[model.ID]
if ok {
// Parse inference timeout only if the string is not empty
if cogConfig.HttpTimeout != "" {
parsedTimeout, err := time.ParseDuration(cogConfig.HttpTimeout)
if err != nil {
logger.Warn().Err(err).Str("model", model.ID).Str("config_timeout", cogConfig.HttpTimeout).Msg("failed to parse model timeout from cog config, using default 120s")
// Keep default timeout
} else {
timeout = parsedTimeout
}
} // Else: HttpTimeout is empty, silently use the default

// Parse IPFS timeout only if the string is not empty
}

if cogConfig.IpfsTimeout != "" {
parsedIpfsTimeout, err := time.ParseDuration(cogConfig.IpfsTimeout)
if err != nil {
logger.Warn().Err(err).Str("model", model.ID).Str("config_ipfs_timeout", cogConfig.IpfsTimeout).Msg("failed to parse IPFS timeout from cog config, using default 30s")
// Keep default ipfsTimeout
} else {
ipfsTimeout = parsedIpfsTimeout
}
} // Else: IpfsTimeout is empty, silently use the default
}
}

// perform validation on the template
templateMeta, ok := ESMFoldV1ModelTemplate.Template.(map[string]any)
if !ok {
logger.Error().Str("model", model.ID).Msg("invalid template format")
Expand Down Expand Up @@ -144,7 +156,7 @@ func NewESMFoldV1Model(client ipfs.IPFSClient, appConfig *config.AppConfig, logg
},
},
ipfs: client,
client: http,
client: httpClient,
logger: logger,
inputFields: inputFields,
}
Expand Down Expand Up @@ -175,72 +187,93 @@ func (m *ESMFoldV1Model) HydrateInput(preprocessedInput map[string]any, seed uin
}
}

var inner ESMFoldV1Input
inner.Sequence, _ = input["sequence"].(string)
var inner ESMFoldV1Prompt
inner.Input.Prompt, _ = input["prompt"].(string)
return inner, nil
}

func (m *ESMFoldV1Model) GetID() string {
return m.Model.ID
}

func (m *ESMFoldV1Model) GetFiles(ctx context.Context, gpu *common.GPU, taskid string, input any) ([]ipfs.IPFSFile, error) {
if err := ctx.Err(); err != nil {
m.logger.Warn().Err(err).Str("task", taskid).Msg("Context canceled before GetFiles execution")
return nil, err
}

inner, ok := input.(ESMFoldV1Input)
if !ok {
return nil, fmt.Errorf("invalid input type: expected ESMFoldV1Input")
}

payload := map[string]string{"sequence": inner.Sequence}
marshaledInput, err := json.Marshal(payload)
if err != nil {
return nil, fmt.Errorf("failed to marshal input: %w", err)
}

endpoint := fmt.Sprintf("%s:8080/predict", strings.TrimSuffix(gpu.Url, "/"))
req, err := http.NewRequestWithContext(ctx, "POST", endpoint, bytes.NewBuffer(marshaledInput))
if err != nil {
return nil, fmt.Errorf("failed to create request: %w", err)
}
req.Header.Set("Content-Type", "application/json")

resp, err := m.client.Do(req)
if err != nil {
if errors.Is(err, context.DeadlineExceeded) {
m.logger.Error().Err(err).Str("task", taskid).Str("gpu", endpoint).Msg("model inference request timed out")
return nil, fmt.Errorf("model inference timed out: %w", err)
}
return nil, fmt.Errorf("failed to POST to GPU: %w", err)
}
defer resp.Body.Close()

if resp.StatusCode != http.StatusOK {
bodyBytes, _ := io.ReadAll(resp.Body)
if resp.StatusCode == http.StatusConflict {
m.logger.Warn().Str("task", taskid).Str("gpu", endpoint).Int("status", resp.StatusCode).Str("body", string(bodyBytes)).Msg("resource busy")
return nil, ErrResourceBusy
}
return nil, fmt.Errorf("server returned non-200 status: %d - %s", resp.StatusCode, string(bodyBytes))
}

pdbData, err := io.ReadAll(resp.Body)
if err != nil {
return nil, fmt.Errorf("failed to read model response body: %w", err)
}

if len(pdbData) == 0 {
return nil, errors.New("model returned empty PDB data")
}

fileName := fmt.Sprintf("%d.%s.pdb", gpu.ID, uuid.New().String())
path := filepath.Join(m.config.CachePath, fileName)
buffer := bytes.NewBuffer(pdbData)

return []ipfs.IPFSFile{{Name: "result.pdb", Path: path, Buffer: buffer}}, nil
func (m *ESMFoldV1Model) GetFiles(ctx context.Context, gpu *common.GPU, taskid string, input interface{}) ([]ipfs.IPFSFile, error) {
if err := ctx.Err(); err != nil {
m.logger.Warn().Err(err).Str("task", taskid).Msg("Context canceled before GetFiles execution")
return nil, err
}

inner, ok := input.(ESMFoldV1Prompt)
if !ok {
return nil, fmt.Errorf("invalid input type: expected ESMFoldV1Prompt")
}

payload := map[string]string{"sequence": inner.Input.Prompt}
marshaledInput, err := json.Marshal(payload)
if err != nil {
return nil, fmt.Errorf("failed to marshal input: %w", err)
}

m.logger.Debug().Str("marshaledInput", string(marshaledInput)).Msg("Prepared input payload")
m.logger.Debug().Str("gpu_url", gpu.Url).Msg("GPU URL")

endpoint := fmt.Sprintf("%s/predict", strings.TrimSuffix(gpu.Url, "/"))
m.logger.Debug().Str("endpoint", endpoint).Msg("Constructed endpoint URL")

tmpFile, err := os.CreateTemp("", "curl_output_*.pdb")
if err != nil {
m.logger.Error().Err(err).Str("task", taskid).Msg("Failed to create temporary file")
return nil, fmt.Errorf("failed to create temporary file: %w", err)
}
tmpFileName := tmpFile.Name()
tmpFile.Close()

curlArgs := []string{
"-v",
"-k",
"-X", "POST",
"-H", "Content-Type: application/json",
"-H", "Accept: chemical/x-pdb",
"-d", string(marshaledInput),
"-o", tmpFileName,
endpoint,
}

m.logger.Debug().Str("curl_command", fmt.Sprintf("curl %s", strings.Join(curlArgs, " "))).Msg("Executing curl")

cmd := exec.CommandContext(ctx, "curl", curlArgs...)
var stderr bytes.Buffer
cmd.Stderr = &stderr
if err := cmd.Run(); err != nil {
m.logger.Error().
Err(err).
Str("task", taskid).
Str("gpu", endpoint).
Str("stderr", stderr.String()).
Msg("Failed to execute curl")
os.Remove(tmpFileName)
return nil, fmt.Errorf("failed to execute curl: %w, stderr: %s", err, stderr.String())
}

pdbData, err := os.ReadFile(tmpFileName)
if err != nil {
m.logger.Error().Err(err).Str("task", taskid).Msg("Failed to read curl output file")
os.Remove(tmpFileName)
return nil, fmt.Errorf("failed to read curl output file: %w", err)
}
os.Remove(tmpFileName)

if len(pdbData) == 0 {
m.logger.Error().Str("task", taskid).Msg("curl returned empty PDB data")
return nil, errors.New("curl returned empty PDB data")
}

m.logger.Debug().Int("data_length", len(pdbData)).Msg("Received curl response")

fileName := fmt.Sprintf("%d.%s.pdb", gpu.ID, uuid.New().String())
path := filepath.Join(m.config.CachePath, fileName)
buffer := bytes.NewBuffer(pdbData)

return []ipfs.IPFSFile{{Name: "result.pdb", Path: path, Buffer: buffer}}, nil
}

func (m *ESMFoldV1Model) GetCID(ctx context.Context, gpu *common.GPU, taskid string, input any) ([]byte, error) {
Expand Down