diff --git a/openfold3/core/data/pipelines/preprocessing/template.py b/openfold3/core/data/pipelines/preprocessing/template.py
index 865939f55..a6aba517e 100644
--- a/openfold3/core/data/pipelines/preprocessing/template.py
+++ b/openfold3/core/data/pipelines/preprocessing/template.py
@@ -14,6 +14,7 @@
 
 """Preprocessing pipelines for template data ran before training/evaluation."""
 
+import getpass
 import logging
 import multiprocessing as mp
 import os
@@ -1602,7 +1603,7 @@ def _prepare_output_directories(self) -> "TemplatePreprocessorSettings":
             )
 
         self.output_directory = (
-            self.output_directory or Path(tempfile.gettempdir()) / "of3_template_data"
+            self.output_directory or Path(tempfile.gettempdir()) / f"of3-{getpass.getuser()}" / "template_data"
         )
         base = self.output_directory
 
diff --git a/openfold3/core/data/tools/colabfold_msa_server.py b/openfold3/core/data/tools/colabfold_msa_server.py
index e4b12f295..4fd053d17 100644
--- a/openfold3/core/data/tools/colabfold_msa_server.py
+++ b/openfold3/core/data/tools/colabfold_msa_server.py
@@ -12,6 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import getpass
 import json
 import logging
 import os
@@ -997,7 +998,7 @@ class MsaComputationSettings(BaseModel):
     server_user_agent: str = "openfold"
     server_url: Url = Url("https://api.colabfold.com")
     save_mappings: bool = True
-    msa_output_directory: Path = Path(tempfile.gettempdir()) / "of3_colabfold_msas"
+    msa_output_directory: Path = Path(tempfile.gettempdir()) / f"of3-{getpass.getuser()}" / "colabfold_msas"
     cleanup_msa_dir: bool = True
 
     @model_validator(mode="after")
diff --git a/openfold3/core/data/tools/jackhmmer.py b/openfold3/core/data/tools/jackhmmer.py
index c400ce42a..9c6896056 100644
--- a/openfold3/core/data/tools/jackhmmer.py
+++ b/openfold3/core/data/tools/jackhmmer.py
@@ -15,11 +15,14 @@
 
 """Library to run Jackhmmer from Python."""
 
+import getpass
 import glob
 import logging
 import os
 import subprocess
+import tempfile
 from collections.abc import Callable, Mapping, Sequence
+from pathlib import Path
 from concurrent import futures
 from typing import Any
 from urllib import request
@@ -203,7 +206,9 @@ def db_remote_chunk(db_idx):
             return f"{self.database_path}.{db_idx}"
 
         def db_local_chunk(db_idx):
-            return f"/tmp/ramdisk/{db_basename}.{db_idx}"
+            ramdisk_dir = Path(tempfile.gettempdir()) / f"of3-{getpass.getuser()}" / "ramdisk"
+            ramdisk_dir.mkdir(parents=True, exist_ok=True)
+            return str(ramdisk_dir / f"{db_basename}.{db_idx}")
 
         # Remove existing files to prevent OOM
         for f in glob.glob(db_local_chunk("[0-9]*")):